Science.gov

Sample records for 2d polyacrylamide gel

  1. Polyacrylamide gel plugs enabling 2-D microfluidic protein separations via isoelectric focusing and multiplexed sodium dodecyl sulfate gel electrophoresis.

    PubMed

    Liu, Jikun; Yang, Shuang; Lee, Cheng S; DeVoe, Don L

    2008-06-01

    In situ photopolymerized polyacrylamide (PAAm) gel plugs are used as hydrodynamic flow control elements in a multidimensional microfluidic system combining IEF and parallel SDS gel electrophoresis for protein separations. The PAAm gel plugs offer a simple method to reduce undesirable bulk flow and limit reagent/sample crosstalk without placing unwanted constraints on the selection of separation media, and without hindering electrokinetic ion migration in the complex microchannel network. In addition to improving separation reproducibility, the discrete gel plugs integrated into critical regions of the chip enable the use of a simple pressure-driven sample injection method which avoids electrokinetic injection bias. The gel plugs also serve to greatly simplify operation of the spatially multiplexed system by eliminating the need for complex external fluidic interfaces. Using an FITC-labeled Escherichia coli cell lysate as a model system, the use of gel plugs is shown to significantly enhance separation reproducibility in a chip containing five parallel CGE channels, with an average variance in peak elution time of only 4.1%. PMID:18449857

  2. Polyacrylamide gel electrophoresis.

    PubMed

    Chrambach, A; Rodbard, D

    1971-04-30

    Polyacrylamide gel electrophoresis (PAGE) provides a versatile, gentle, high resolution method for fractionation and physical-chemical characterization of molecules on the basis of size, conformation, and net charge. The polymerization reaction can be rigorously controlled to provide uniform gels of reproducible, measurable pore size over a wide range. This makes it possible to obtain reproducible relative mobility (Rf) values as physical-chemical constants. Application and extension of Ogston's (random fiber) model for a gel allows for calculation of molecular volume, surface area, or radius, free mobility, and valence from RJ measurements at several gel concentrations, to calculate gel concentration for optimal resolution, and to predict behavior of macromolecules on gel gradients by computerized methods. Extension of classical moving boundary theory has been used to generate multiphasic buffer systems (providing selective stacking, unstacking, restacking, and preparative steady-state-stacking) with known operating characteristics for any pH at 0 degrees and 25 degrees C. A general strategy for isolation of macromolecules and for macromolecular mapping has been developed. Preparative scale PAGE is operational for milligram loads and feasible for gram quantities. PMID:4927678

  3. The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis.

    PubMed Central

    Appel, R D; Sanchez, J C; Bairoch, A; Golaz, O; Ravier, F; Pasquali, C; Hughes, G J; Hochstrasser, D F

    1994-01-01

    SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), created and maintained at the University Hospital of Geneva in collaboration with the Department of Medical Biochemistry of Geneva University. The proteins have been identified on various 2-D PAGE reference maps by microsequencing, immunoblotting, gel comparison and amino acid composition. Images PMID:7937063

  4. Silver staining of proteins in polyacrylamide gels

    PubMed Central

    Chevallet, Mireille; Luche, Sylvie; Rabilloud, Thierry

    2006-01-01

    Silver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels. It combines excellent sensitivity (in the low nanogram range) whilst using very simple and cheap equipment and chemicals. It is compatible with downstream processing such as mass spectrometry analysis after protein digestion. The sequential phases of silver staining are protein fixation, then sensitization, then silver impregnation and finally image development. Several variants of silver staining are described here, which can be completed in a time range from 2 hours to one day after the end of the electrophoretic separation. Once completed, the stain is stable for several weeks PMID:17487168

  5. Enhanced detection of glycoproteins in polyacrylamide gels.

    PubMed

    Muñoz, G; Marshall, S; Cabrera, M; Horvat, A

    1988-05-01

    A highly sensitive and simple method to enhance detection of glycoproteins resolved by either one- or two-dimensional polyacrylamide gel electrophoresis is described. The method is a modification of the procedure described by D. Fargeaud et al. (D. Fargeaud, J. C. Benoit, F. Kato, and G. Chappuis (1984) Arch. Virol. 80, 69-82) that uses concanavalin A conjugated with fluorescein isothyocyanate to detect the carbohydrate moiety of glycoproteins. Briefly, the electrophoresed gel is exposed to the fluorescent lectin, thoroughly washed, and sequentially transferred to 50% methanol in deionized water and to absolute methanol. The result is an abrupt dehydration of the gel which turns evenly white and stiff. At least a twofold enhancement of fluorescence is obtained as detected by exposing the treated gel to an appropriate uv source. The sensitivity of the procedure allows us to detect purified immunoglobulin molecules by their carbohydrate content in the range of 0.2 microgram of total protein. The specificity of the detection is demonstrated by a comparison with the corresponding polypeptide profile obtained by silver nitrate staining of the gel. PMID:3394948

  6. Micro-size polyacrylamide gel electrophoresis system

    NASA Astrophysics Data System (ADS)

    Hinson, W. G.; Pipkin, J. L.; Anson, J. F.; Casciano, D. A.; Burns, E. R.

    1987-09-01

    The development and characterization of a micro-size two-dimensional polyacrylamide gel electrophoresis system is described. Some of the techniques which have evolved with use of the system are also discussed. This apparatus has unique features which provide advantages over other small scale units. Up to ten first- and second-dimension gels can be processed simultaneously with excellent resolution of protein regions. Consistent reproducibility is possible from protein samples as small as 400 ng and individual protein regions as small as 1 pg can be visualized by silver staining of the two-dimensional gels. Similar sensitivities are achieved in autoradiographs of 3H-labeled proteins extracted from the nuclei of cultured cells. The application of this system in conjunction with flow cytometric examination of nuclear DNA and electrostatic cell sorting of specific cell nuclei to provide homogeneous sample populations, allows subtle variations in isotope incorporation in proteins to be detected; whereas many times in generalized tissue samples these changes are masked. Also, these techniques elucidate the effects of external stimuli (chemicals, drugs, or environment) on protein synthesis and phosphorylation for analyses and comparison. Fabrication drawings are available upon request.

  7. The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995.

    PubMed Central

    Appel, R D; Sanchez, J C; Bairoch, A; Golaz, O; Ravier, F; Pasquali, C; Hughes, G J; Hochstrasser, D F

    1996-01-01

    SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The current release contains 343 entries of human, yeast (Saccharomyces cerevisiae) and Escherichia coli origin, as well as virtual entries for each of the protein sequences in the SWISS-PROT database. PMID:8594575

  8. Purification of DNA Oligos by denaturing polyacrylamide gel electrophoresis (PAGE).

    PubMed

    Lopez-Gomollon, Sara; Nicolas, Francisco Esteban

    2013-01-01

    After chemical synthesis, the oligonucleotide preparation contains the desired full-length oligonucleotide but also all of the DNA molecules that were aborted during each cycle in the synthesis, and the by-products generated during the chemical reactions. The purification of oligonucleotides is a critical step for demanding applications where the exact length or sequence of the oligonucleotide is important, or for oligonucleotides longer than 50 bases. There are several methods of increasing oligonucleotide purity, the choice of which will depend on modifications of the oligonucleotides and their intended use. Polyacrylamide gel purification (PAGE purification) is the method of choice when the highest percentage of full-length oligonucleotide is desired. This chapter describes a protocol for oligonucleotide purification using denaturing polyacrylamide gel electrophoresis, and includes oligonucleotide preparation, polyacrylamide gel electrophoresis, and purification from the gel slice by two different methods: by diffusion or by electroelution. This chapter also includes recommendations as well as protocol advice. PMID:24011037

  9. Further characterization of filarial antigens by SDS polyacrylamide gel electrophoresis

    PubMed Central

    Dissanayake, S.; Galahitiyawa, S. C.; Ismail, M. M.

    1983-01-01

    SDS (sodium dodecyl sulfate)-polyacrylamide gel electrophoresis of an antigen isolated from sera of Wuchereria bancrofti-infected patients and Setaria digitata antigen SD2-4 is reported. Both antigens showed carbohydrate (glycoprotein) staining. The W. bancrofti antigen had an apparent relative molecular mass of 35 000 while the S. digitata antigen SD2-4 migrated at the marker dye position on SDS-polyacrylamide gel electrophoresis. SDS treatment of these antigens did not abolish the precipitation reaction with antibody. In the case of W. bancrofti antigen, SDS treatment probably exposed hitherto hidden antigen epitopes. PMID:6354508

  10. Detection of glutathione transferase activity on polyacrylamide gels.

    PubMed

    Ricci, G; Lo Bello, M; Caccuri, A M; Galiazzo, F; Federici, G

    1984-12-01

    A simple and sensitive assay for glutathione transferase activity on polyacrylamide gel is described. The method is based on the fast reduction of nitroblue tetrazolium salt by glutathione. Blue insoluble formazan colors the gel except in the glutathione transferase area. The stable and defined colorless zone is still detectable with 0.005 unit enzyme. This technique has been successfully applied with enzyme preparations of human heart and other tissues. PMID:6532239

  11. 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. PMID:20235459

  12. Complications of breast augmentation with injected hydrophilic polyacrylamide gel.

    PubMed

    Cheng, Ning-Xin; Wang, Yuan-Lu; Wang, Jin-Huang; Zhang, Xiao-Man; Zhong, Hong

    2002-01-01

    Since 1997, the hydrophilic polyacrylamide gel (PAAG), an injectable alloplastic biomaterial, imported from the Ukraine has been used for augmentation mammaplasty in China. There were twelve patients with various complications visiting our hospitals after breast augmentation with injected hydrophilic polyacrylamide gel by other clinics, even though such procedures are not performed in our clinical practices. The complications included four cases of PAAG-induced multiple induration and lumps, and one with lactation, three cases of hematoma, two cases of inflammation (infection), and persistent mastodymia, unsatisfactory contour results and abnormal skin sensations in each case. All patients have been treated by removing the injected gel and giving antibiotics. Other procedures included replacement by silicon breast prostheses, mammotomy, and segmental mastectomy. We suggest that the injectable hydrophilic polyacrylamide gel be contraindications for breast augmentation in any young female who is not married, or without a child, with a tendency to hemorrhage, and with little mammary tissue. Some considerations to prevent and manage these complications are discussed. PMID:12432479

  13. The electrophoresis of transferrins in urea/polyacrylamide gels.

    PubMed Central

    Evans, R W; Williams, J

    1980-01-01

    The denaturation of transferrin by urea has been studied by (a) electrophoresis in polyacrylamide gels incorporating a urea gradient, (b) measurements of the loss of iron-binding capacity and (c) u.v. difference spectrometry. In human serum transferrin and hen ovotransferrin the N-terminal and C-terminal domains of the iron-free protein were found to denature at different urea concentrations. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 7. PMID:7213345

  14. Basics and recent advances of two dimensional- polyacrylamide gel electrophoresis

    PubMed Central

    2014-01-01

    Gel- based proteomics is one of the most versatile methods for fractionating protein complexes. Among these methods, two dimensional- polyacrylamide gel electrophoresis (2-DE) represents a mainstay orthogonal approach, which is popularly used to simultaneously fractionate, identify, and quantify proteins when coupled with mass spectrometric identification or other immunological tests. Although 2-DE was first introduced more than three decades ago, several challenges and limitations to its utility still exist. This review discusses the principles of 2-DE as well as both recent methodological advances and new applications. PMID:24735559

  15. Polyacrylamide Gel Electrophoresis for Purification of Large Amounts of RNA.

    PubMed

    Meyer, Mélanie; Masquida, Benoît

    2016-01-01

    Polyacrylamide gel electrophoresis (PAGE) constitutes a powerful technique for the efficient purification of RNA molecules dedicated to applications that require high purity levels. PAGE allows for the fractionation of RNA obtained from cell extracts, chemical or enzymatic synthesis, or modification experiments. Native or denaturing conditions can be chosen for analytical or preparative-scale separations and the nucleotide resolution can be tuned by changing the percentage and reticulation of the gel material. In this protocol, we focus on the preparation of milligram-scale amounts of ~200 nucleotides (nt) RNA molecules that were used in subsequent crystallization experiments. PMID:26227037

  16. 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.

  17. Aggregative properties of Rhodamine dyes in polyacrylamide hydrophilic gel media

    NASA Astrophysics Data System (ADS)

    Zakerhamidi, M. S.; Moghadam, M.; Karimi, A.

    2013-02-01

    The visible absorption spectra of two Rhodamine dyes (R6G and RB) in aqueous solutions, and in the polyacrylamide hydrogel matrix with different composition were studied at room temperature. The spectral properties of the dye-loaded hydrogel were also investigated. The transport and the solute-solute interactions of the ionic dyes in aqueous solutions across the hydrophilic gels were calculated. The monomer-dimer equilibrium of these ionic dyes in water and in different composition of hydrogel environment with different soaking time has been investigated by means of UV-Vis spectroscopy. The natures of the interacting pairs in these dyes were discussed using the Kasha exciton theory.

  18. Separation of radiolabelled glycosaminoglycan oligosaccharides by polyacrylamide-gel electrophoresis.

    PubMed Central

    Hampson, I N; Gallagher, J T

    1984-01-01

    Glycosaminoglycan oligosaccharides generated by treatment of biosynthetically radiolabelled dermatan sulphate and hyaluronic acid with chondroitin AC lyase or testicular hyaluronidase may be resolved into a series of discrete bands by polyacrylamide-gel electrophoresis. Bands were identified by fixation in glacial acetic acid containing 20% (w/v) 2,5-diphenyloxazole followed by fluorography. The bands represented glycans which differed in size by one disaccharide unit. For the larger oligosaccharides (decasaccharides and above) of similar charge: mass ratio, there was a linear relationship between electrophoretic mobility and log Mr. However, the smaller species showed anomalous migration patterns. Consideration of the structures of the fragments produced by the different enzyme treatments suggests that copolymeric and homopolymeric oligosaccharides may be separated by polyacrylamide-gel electrophoresis. There are many potential applications of this technique, foremost amongst them being studies on the molecular size heterogeneity and patterns of enzyme-mediated depolymerization of native glycosaminoglycan chains and investigations into rates of polymer chain elongation and post-polymerization modification reactions so essential to glycosaminoglycan function. Images Fig. 1. Fig. 2. Fig. 5. Fig. 6. PMID:6477495

  19. Physical properties of polyacrylamide gels probed by AFM and rheology

    NASA Astrophysics Data System (ADS)

    Abidine, Yara; Laurent, Valérie M.; Michel, Richard; Duperray, Alain; Iulian Palade, Liviu; Verdier, Claude

    2015-02-01

    Polymer gels have been shown to behave as viscoelastic materials but only a small amount of data is usually provided in the glass transition. In this paper, the dynamic moduli G\\prime and G\\prime\\prime of polyacrylamide hydrogels are investigated using both an AFM in contact force modulation mode and a classical rheometer. The validity is shown by the matching of the two techniques. Measurements are carried out on gels of increasing polymer concentration in a wide frequency range. A model based on fractional derivatives is successfully used, covering the whole frequency range. G\\text{N}0 , the plateau modulus, as well as several other parameters are obtained at low frequencies. The model also predicts the slope a of both moduli in the glass transition, and a transition frequency f\\text{T} is introduced to separate the gel-like behavior with the glassy state. Its variation with polymer content c gives a dependence f\\text{T}∼ c1.6 , in good agreement with previous theories. Therefore, the AFM data provides new information on the physics of polymer gels.

  20. Characteristics of polyacrylamide gel with THPC and Turnbull Blue gel dosimeters evaluated using optical tomography

    NASA Astrophysics Data System (ADS)

    Pilařová (Vávrů), Kateřina; Kozubíková, Petra; Šolc, Jaroslav; Spěváček, Václav

    2014-11-01

    The purpose of this study was to compare characteristics of radiochromic gel - Turnbull Blue gel (TB gel) with polymer gel - polyacrylamide gel and tetrakis hydroxymethyl phosphonium chloride (PAGAT) using optical tomography. Both types of gels were examined in terms of dose sensitivity, dose response linearity and background value of spectrophotometric absorbance. The calibration curve was obtained for 60Co irradiation performed on Gammacell 220 at predefined gamma dose levels between 0 and 140 Gy for TBG and 0-15 Gy for PAGAT. To measure relative dose distributions from stereotactic irradiation, dosimeters were irradiated on Leksell Gamma Knife Perfexion. The cylindrical glass housings filled with gel were attached to the stereotactic frame. They were exposed with single shot and 16 mm collimator by 65 Gy to a 50% prescription isodose for TB gel and 4 Gy to a 50% prescription isodose for PAGAT. Evaluations of dosimeters were performed on an UV-vis Spectrophotometer Helios β and an optical cone beam homemade tomography scanner with a 16-bit astronomy CCD camera with a set of color filters. The advantages and potential disadvantages for both types of gel dosimeters were summarized. Dose distribution in central slice and measured profiles of 16 mm shot shows excellent correspondence with treatment planning system Leksell GammaPlan® for both PAGAT and Turnbull Blue gels. Gel dosimeters are suitable for steep dose gradient verification. An optical tomography evaluation method is successful. Dose response characteristics of TB gel and PAGAT gel are presented.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  2. [Detection of picobirnaviruses by electrophoresis of RNA in polyacrylamide gel].

    PubMed

    Novikova, N A; Epifanova, N V; Fedorova, O F; Golitsyna, L N; Kupriianova, N V

    2003-01-01

    Double-segment profiles typical of picobirnavirus (PBV) were detected (during 1994-2001) in nucleic acids extracted from feces of children (3 cases) and calf (1 case) with diarrhea by using the method of electrophoresis. The human genomic PBV segments migrated in the polyacrylamide gel (PAAG) as dsRNA segments sized 1.7 and 2.4 kbp for small and large segments, respectively; the similar calf sizes were 1.5 and 2.6 kbp. PBVs were detected in various places of the Nizhny Novgorod Region and at different time periods. It was for the first time that the PBV circulation was proven to be present in Russia's territory. However, their association with diarrhea was not reliably established, and the pathogenic PBV potential needs further investigations. PMID:14708231

  3. Scalable lithography from Natural DNA Patterns via polyacrylamide gel

    PubMed Central

    Qu, JieHao; Hou, XianLiang; Fan, WanChao; Xi, GuangHui; Diao, HongYan; Liu, XiangDon

    2015-01-01

    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. PMID:26639572

  4. 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.

  5. Scalable lithography from Natural DNA Patterns via polyacrylamide gel.

    PubMed

    Qu, JieHao; Hou, XianLiang; Fan, WanChao; Xi, GuangHui; Diao, HongYan; Liu, XiangDon

    2015-01-01

    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. PMID:26639572

  6. Low temperature synthesis of nanocrystalline YVO 4:Eu via polyacrylamide gel method

    NASA Astrophysics Data System (ADS)

    Zhang, Hongwu; Fu, Xiaoyan; Niu, Shuyun; Sun, Gongquan; Xin, Qin

    2004-08-01

    Nanocrystalline europium doped yttrium orthovanadate (YVO 4:Eu) were synthesized by the polyacrylamide gel method. For a comparative evaluation, bulk YVO 4:Eu was prepared by solid-state reaction. On the basis of X-ray powder diffraction, scanning and transmission electron microscopy and luminescence measurements, the polyacrylamide gel method appears to be a more efficient method to prepare the luminescence materials YVO 4:Eu with high homogeneity, purity and luminescence intensity.

  7. 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. PMID:26826592

  8. A versatile polyacrylamide gel electrophoresis based sulfotransferase assay

    PubMed Central

    2010-01-01

    Background Sulfotransferases are a large group of enzymes that regulate the biological activity or availability of a wide spectrum of substrates through sulfation with the sulfur donor 3'-phosphoadenosine-5'-phosphosulfate (PAPS). These enzymes are known to be difficult to assay. A convenient assay is needed in order to better understand these enzymes. Results A universal sulfotransferase assay method based on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) is described. This assay has been successfully applied to substrates as small as α-naphthol and as big as proteoglycans. As examples, we present the assays for recombinant human CHST4, TPST1, CHST3 and HS6ST1. In order to assess whether a small molecule can be applicable to this type of assay, a method to estimate the relative mobility of a molecule to PAPS is also presented. The estimated relative mobilities of various sulfated small molecules generated by SULT1A1, SULT1E1, SULT2A1 and CHST4 are in the range of ± 0.2 of the actual relative mobilities. Conclusion The versatility of the current method comes from the ability that SDS-PAGE can separate proteins and small molecules according to different parameters. While mobilities of proteins during SDS-PAGE are inversely related to their sizes, mobilities of small molecules are positively related to their charge/mass ratios. The predicted relative mobility of a product to PAPS is a good indicator of whether a sulfotransferase can be assayed with SDS-PAGE. Because phosphorylation is most similar to sulfation in chemistry, the method is likely to be applicable to kinases as well. PMID:20146816

  9. Spot identification on 2D electrophoresis gel images

    NASA Astrophysics Data System (ADS)

    Wang, Weixing

    2006-09-01

    2-D electrophoresis gel images can be used for identifying and characterizing many forms of a particular protein encoded by a single gene. Conventional approaches to gel analysis require the three steps: (1) Spot detection on each gel; (2) Spot matching between gels; and (3) Spot quantification and comparison. Many researchers and developers attempt to automate all steps as much as possible, but errors in the detection and matching stages are common. In order to carry out gel image analysis, one first needs to accurately detect and measure the protein spots in a gel image. This paper presents the algorithms for automatically delineating gel spots. The fusion of two types of segmentation algorithms was implemented. One is edge (discontinuity) based type, and the other is region based type. The primary integration of the two types of image segmentation algorithms have been tested too, the test results clearly show that the integrated algorithm can automatically delineate gel spots not only on a simple image and also on a complex image, and it is much better that either only edge based algorithm or only region based algorithm. Based on the testing and analysis results, the fusion of edge information and region information for gel image segmentation is good for this kind of images.

  10. 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. PMID:7864363

  11. Optimal parameters for laccase-mediated destaining of Coomassie Brilliant Blue R-250-stained polyacrylamide gels.

    PubMed

    Yang, Jie; Yang, Xiaodan; Ye, Xiuyun; Lin, Juan

    2016-06-01

    The data presented in this article are related to the research article entitled "Destaining of Coomassie Brilliant Blue R-250-stained polyacrylamide gels with fungal laccase" [1]. Laccase is a class of multicopper oxidases that can catalyze oxidation of recalcitrant dyestuffs. This article describes optimal parameters for destaining of polyacrylamide gels, stained with Coomassie Brilliant Blue R-250, with laccase from basidiomycete Cerrena sp. strain HYB07. Effects of laccase activity, mediator type and concentration, temperature and time on destaining of polyacrylamide gels were evaluated with respect to gel background intensity and protein band signals, and the optimal destaining effects were obtained with 15 U mL(-1) laccase and 2 μM ABTS at 37 °C after 2 h. PMID:26955647

  12. Band broadening of DNA fragments isolated by polyacrylamide gel electrophoresis in capillary electrophoresis.

    PubMed

    Kaneta, Takashi; Ogura, Takehito; Yamato, Shuhei; Imasaka, Totaro

    2012-02-01

    Polyacrylamide gel electrophoresis (PAGE) is used frequently for isolation and purification of DNA fragments. In the present study, DNA fragments extracted from polyacrylamide gels showed significant band broadening in capillary electrophoresis (CE). A pHY300PLK (a shuttle vector functioning in Escherichia coli and Bacillus subtilis) marker, which contained nine fragments ranging from 80 to 4870 bp, was separated by PAGE, and each fragment was isolated by phenol/chloroform extraction and ethanol precipitation. After extraction from the polyacrylamide gel, the peaks of the isolated DNA fragments exhibited band broadening in CE, where a linear poly(ethylene oxide) was used as a sieving matrix. The theoretical plate numbers of the DNA fragments contained in the pHY300PLK marker were >10(6) for all the fragments before extraction. However, the DNA fragments extracted from the polyacrylamide gel showed decreased theoretical plate numbers (5-20 times smaller). The degradation of the theoretical plate number was significant for middle sizes of the DNA fragments ranging from 489 to 1360 bp, whereas the largest and smallest fragments (80 and 4870 bp) had no obvious influence. The band broadening was attributed to contamination of the DNA fragments by polyacrylamide fibers during the separation and extraction process. PMID:22258810

  13. Polyacrylamide gel in cosmetic procedures: experience with Aquamid.

    PubMed

    Patrick, Trevidic

    2004-12-01

    Polyacrylamides have been used in tissue augmentation since 1980. AQUAMID injections amounting to 40,000 have been done for facial and body corrections in cosmetic and reconstructive medicine and surgery. Possible neurotoxic and carcinologic effects of acrylamide and their stability are reported. The most important complications are infection, granuloma, and migration. All actual studies and results are reported. Main indications are lips, nasolabial fold, and malar area. PMID:15745231

  14. Sodium dodecyl sulfate-capillary gel electrophoresis of proteins using non-cross-linked polyacrylamide.

    PubMed

    Wu, D; Regnier, F E

    1992-09-11

    Proteins with relative molecular masses of 14,000 to 205,000 were separated by sodium dodecyl sulfate-capillary gel electrophoresis (SDS-CGE) using non-cross-linked linear polyacrylamide gels on both coated and uncoated fused-silica capillaries. It was determined that viscosity of the acrylamide solution was a major factor affecting column stability with linear acrylamide gels. When the viscosity of the acrylamide solution reaches 100 cP, electro-osmotically driven displacement of the gels is insignificant. Uncoated capillaries provided better resolution, stability, and reproducibility than surface coated capillaries when the concentration of linear polyacrylamide was greater than 4%. At lower gel concentrations, non-cross-linked polyacrylamide is easily displaced from the columns. A calibration plot of log molecular mass vs. mobility with non-linear polyacrylamide was linear, which indicated that resolution was equivalent to that obtained with cross-linked acrylamide. Separations with model proteins indicated that baseline resolution between protein species that vary 10% in molecular mass can be achieved. PMID:1430034

  15. Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA-oligonucleotide microchips.

    SciTech Connect

    Proudnikov, D.; Timofeev, E.; Mirzabekov, A.; Center for Mechanistic Biology and Biotechnology; Engelhardt Inst. of Molecular Biology

    1998-05-15

    Activated DNA was immobilized in aldehyde-containing polyacrylamide gel for use in manufacturing the MAGIChip (microarrays of gel-immobilized compounds on a chip). First, abasic sites were generated in DNA by partial acidic depurination. Amino groups were then introduced into the abasic sites by reaction with ethylenediamine and reduction of the aldimine bonds formed. It was found that DNA could be fragmented at the site of amino group incorporation or preserved mostly unfragmented. In similar reactions, both amino-DNA and amino-oligonucleotides were attached through their amines to polyacrylamide gel derivatized with aldehyde groups. Single- and double-stranded DNA of 40 to 972 nucleotides or base pairs were immobilized on the gel pads to manufacture a DNA microchip. The microchip was hybridized with fluorescently labeled DNA-specific oligonucleotide probes. This procedure for immobilization of amino compounds was used to manufacture MAGIChips containing both DNA and oligonucleotides.

  16. One-dimensional SDS-polyacrylamide gel electrophoresis (1D SDS-PAGE).

    PubMed

    Brunelle, Julie L; Green, Rachel

    2014-01-01

    This protocol describes a denaturing polyacrylamide gel system utilizing sodium dodecyl sulfate (SDS) to separate protein molecules based on size as first described by Laemmli (1970). SDS-PAGE can be used to monitor protein purifications, check the purity of samples, and to estimate molecular weights for unknown proteins. PMID:24674069

  17. [Protein analysis of 6 crude drugs and their processed products by polyacrylamide gel electrophoresis technique].

    PubMed

    Shi, J; Sun, L; Jing, X

    1995-09-01

    In this paper, the proteins in 6 crude drugs (Prunus persica; P. armeniaca; Dolichos lablab; Strychnos nux-vomica; Mylabris phalerata; Whitmania pigra) and their processed products were analysed by polyacrylamide gel electrophoresis technique, and the effect of different processing methods on the quantity and kind of protein was explored. Protein electrophorograms of 20 samples are drawn. PMID:8679088

  18. Highly sensitive method for specific, brief, and economical detection of glycoproteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis by the synthesis of a new hydrazide derivative.

    PubMed

    Cong, Weitao; Zhou, Ayi; Liu, Zhiguo; Shen, Jiayi; Zhou, Xuan; Ye, Weijian; Zhu, Zhongxin; Zhu, Xinliang; Lin, Jianjun; Jin, Litai

    2015-02-01

    A new hydrazide derivative was synthesized and used for the first time as a specific, brief, and economical probe to selectively visualize glycoproteins in 1-D and 2-D sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with high sensitivity. The detection limit of the newly developed staining method is 2- and 4-fold higher than that of the widely used Pro-Q Emerald 300 and 488 stains, respectively. PMID:25565298

  19. Renaturation of enzymes after polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate

    SciTech Connect

    Lacks, S.A.; Springhorn, S.S.

    1980-08-10

    A number of enzymes, including amylases, dehydrogenases, and proteases, were shown to be renaturable after polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. Enzyme activity was detected in situ by action on substrates introduced into the gel and subsequent staining of either the product or unreacted substrate. Enzymes appeared to recover activity as soon as the detergent diffused out of the gel. Renatured enzymes were retained in gels after electrophoresis longer than native enzymes which had been subjected to electrophoresis in the absence of detergent. Re-electrophoresis of the renatured enzymes showed that part of the retained activity was physically anchored to the gel, possibly by the folding of polypeptides around the gel matrix as the enzymes were renatured.

  20. Polyacrylamide gel electrophoretic methods in the separation of structural muscle proteins.

    SciTech Connect

    Barany, K.; Barany, M.; Giometti, C. S.; Center for Mechanistic Biology and Biotechnology; Univ. of Illinois at Chicago

    1995-04-28

    Polyacrylamide gel electrophoresis plays a major role in analyzing the function of muscle structural proteins. This review describes one- and two-dimensional gel electrophoretic methods for qualitative and quantitative investigation of the muscle proteins, with special emphasis on determination of protein phosphorylation. The electrophoretic studies established the subunit structures of the muscle proteins, characterized their multiple forms, revealed changes in subunit composition or shifts in isoform distribution of specific proteins during development, upon stimulation or denervation of the muscle. Protein phosphorylation during muscle contraction is preferentially studied by two-dimensional gel electrophoresis. The same method demonstrated protein alterations in human neuromuscular diseases.

  1. Rheological and mechanical behavior of polyacrylamide hydrogels chemically crosslinked with allyl agarose for two-dimensional gel electrophoresis.

    PubMed

    Suriano, R; Griffini, G; Chiari, M; Levi, M; Turri, S

    2014-02-01

    Two-dimensional (2-D) gel electrophoresis currently represents one of the most standard techniques for protein separation. In addition to the most commonly employed polyacrylamide crosslinked hydrogels, acrylamide-agarose copolymers have been proposed as promising systems for separation matrices in 2-D electrophoresis, because of the good resolution of both high and low molecular mass proteins made possible by careful control and optimization of the hydrogel pore structure. As a matter of fact, a thorough understanding of the nature of the hydrogel pore structure as well as of the parameters by which it is influenced is crucial for the design of hydrogel systems with optimal sieving properties. In this work, a series of acrylamide-based hydrogels covalently crosslinked with different concentrations of allyl agarose (0.2-1%) is prepared and characterized by creep-recovery measurements, dynamic rheology and tensile tests, in the attempt to gain a clearer understanding of structure-property relationships in crosslinked polyacrylamide-based hydrogels. The rheological and mechanical properties of crosslinked acrylamide-agarose hydrogels are found to be greatly affected by crosslinker concentration. Dynamic rheological tests show that hydrogels with a percentage of allyl agarose between 0.2% and 0.6% have a low density of elastically effective crosslinks, explaining the good separation of high molecular mass proteins in 2-D gel electrophoresis. Over the same range of crosslinker concentration, creep-recovery measurements reveal the presence of non-permanent crosslinks in the hydrogel network that justifies the good resolution of low molecular mass proteins as well. In tensile tests, the hydrogel crosslinked with 0.4% of allyl agarose exhibits the best results in terms of mechanical strength and toughness. Our results show how the control of the viscoelastic and the mechanical properties of these materials allow the design of mechanically stable hydrogels with improved

  2. Detection of protein kinase activity by renaturation in sodium dodecyl sulfate-polyacrylamide gels

    SciTech Connect

    Anostario, M. Jr.; Harrison, M.L.; Geahlen, R.L.

    1986-05-01

    The authors have developed a procedure for identifying protein kinase activity in protein samples following electrophoresis on SDS-polyacrylamide gels. Proteins are allowed to renature directly in the gel by removal of detergent. The gel is then incubated with (..gamma..-/sup 32/P)ATP to allow renatured protein kinases to autophosphorylate or to phosphorylate various substrates which can be incorporated into the gel. The positions of the radiolabeled proteins can then be detected by autoradiography. With this technique, using purified catalytic subunit of cAMP-dependent protein kinase, enzyme concentrations as low as 0.01 ..mu..g can be detected on gels containing 1.0 mg/ml casein. The procedure is also applicable for the determination of active subunits of multisubunit protein kinases. For example, when the two subunits of casein kinase II are separated by SDS-polyacrylamide gel electrophoresis and allowed to renature, only the larger ..cap alpha.. subunit shows activity. This procedure can also be used to detect and distinguish kinases present in heterogeneous mixtures. Starting with a particulate fraction from LSTRA, a murine T cell lymphoma, several distinct enzymes were detected, including a 30,000 Dalton protein with protein-tyrosine kinase activity. This same enzyme has also been detected in T lymphocytes and other T lymphoid cell lines.

  3. 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. PMID:22585523

  4. Polyacrylamide gel breast augmentation: report of two cases and review of the literature.

    PubMed

    Margolis, Nathaniel E; Bassiri-Tehrani, Brian; Chhor, Chloe; Singer, Cory; Hernandez, Osvaldo; Moy, Linda

    2015-01-01

    Polyacrylamide gel (PAAG) injection remains an uncommon method of breast augmentation. Providers must recognize the clinical and radiological manifestations to optimize management. The clinical and radiological findings of PAAG injection may mimic malignancy and silicone breast augmentation. We described two patients with prior PAAG breast augmentation with physical exam and imaging findings concerning for malignancy. We reviewed the literature on PAAG breast augmentation and compare PAAG to silicone breast augmentation. The management of such patients is discussed. PMID:25670236

  5. Polyacrylamide Slab Gel Electrophoresis of Soluble Proteins for Studies of Bacterial Floras

    PubMed Central

    Moore, W. E. C.; Hash, D. E.; Holdeman, Lillian V.; Cato, Elizabeth P.

    1980-01-01

    A polyacrylamide slab gel electrophoresis procedure was used to compare cellular proteins from bacterial isolates of gingival crevice floras. Isolates with identical protein patterns consistently were shown to be members of the same species. When used to screen isolates, the procedure reduced total analytical time and expense without sacrificing accuracy, and it provided additional verification of the identity of strains characterized by conventional phenotypic tests. Images PMID:16345555

  6. Highly sensitive fluorescent stain for detecting lipopolysaccharides in sodium dodecyl sulfate polyacrylamide gel electrophoresis.

    PubMed

    Wang, Xu; Zhou, Ayi; Cai, Wanhui; Yu, Dongdong; Zhu, Zhongxin; Jiang, Chengxi; Jin, Litai

    2015-08-01

    A sensitive and simple technique was developed for the visualization of gel-separated lipopolysaccharides by using a hydrazide derivative, UGF202. As low as 0.5-1 ng total LPS could be detected by UGF202 stain, which is 2- and 16-fold more sensitive than that of the commonly used Pro-Q Emerald 300 and Keenan et al. developed silver stain, respectively. The results indicated that UGF202 stain could be a good choice for LPS determination in polyacrylamide gels. PMID:25930092

  7. Detection of Connexins in Liver Cells Using Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis and Immunoblot Analysis.

    PubMed

    Willebrords, Joost; Maes, Michaël; Yanguas, Sara Crespo; Cogliati, Bruno; Vinken, Mathieu

    2016-01-01

    Since connexin expression is partly regulated at the protein level, immunoblot analysis represents a frequently addressed technique in the connexin research field. The present chapter describes the setup of an immunoblot procedure, including protein extraction and quantification from biological samples, gel electrophoresis, protein transfer, and immunoblotting, which is optimized for analysis of connexins in liver tissue. In essence, proteins are separated on a polyacrylamide gel using sodium dodecyl sulfate followed by transfer of proteins on a nitrocellulose membrane. The latter allows specific detection of connexins with antibodies combined with revelation through enhanced chemiluminescence. PMID:27207285

  8. Detection of connexins in liver cells using sodiumdodecylsulfate polyacrylamide gel electrophoresis and immunoblot analysis

    PubMed Central

    Willebrords, Joost; Maes, Michaël; Yanguas, Sara Crespo; Cogliati, Bruno; Vinken, Mathieu

    2016-01-01

    Summary Since connexin expression is partly regulated at the protein level, immunoblot analysis represents a frequently addressed technique in the connexin research field. The present chapter describes the set-up of an immunoblot procedure, including protein extraction and quantification from biological samples, gel electrophoresis, protein transfer and immunoblotting, which is optimized for analysis of connexins in liver tissue. In essence, proteins are separated on a polyacrylamide gel using sodiumdodecylsulfate followed by transfer of proteins on a nitrocellulose membrane. The latter allows specific detection of connexins with antibodies combined with revelation through enhanced chemiluminescence. PMID:27207285

  9. The determination of molecular weights of biologically active proteins by cetyltrimethylammonium bromide-polyacrylamide gel electrophoresis.

    PubMed

    Akin, D T; Shapira, R; Kinkade, J M

    1985-02-15

    A novel cetyltrimethylammonium bromide-polyacrylamide gel electrophoresis system which is useful for the separation of native forms of proteins consistent with their molecular weights is reported here. Many proteins examined in this system demonstrated the same association patterns which have been shown by other techniques to exist under nondenaturing conditions. In addition, biological activity could be assayed directly in the gel after electrophoresis. Based on the peculiar characteristics of cetyltrimethylammonium bromide, a possible explanation which may account for the behavior of proteins in this system is presented. PMID:4003759

  10. A Systematic Study of Single-stranded DNA Electrophoresis in Photopolymerized Crosslinked Polyacrylamide Gels

    NASA Astrophysics Data System (ADS)

    Lo, Roger

    2005-03-01

    In this paper, we present a systematic investigation of mobility, diffusion, and dispersion in crosslinked polyacrylamide gels through parallel use of an automated DNA sequencer and a microfabricated electrophoresis device with integrated on-chip electrodes, heaters, and temperature sensors. DNA separations are conducted using the same sample, gel formulations, and operating conditions in both platforms. The microfabricated electrophoresis chip make it possible to collect a complete set of diffusion and dispersion data within about one hour, while it takes several days to finish the same work using a traditional sequencer under the same experimental conditions. By comparing data collected from these two platforms, we can isolate key parameters governing separation performance in both systems. These experimental results are compared with reptation theory to extract information on the gel structure and also predict achievable separation resolution under various operating conditions. We also investigate the effects of gel composition and polymerization chemistry and find that these photopolymerized crosslinked polyacrylamide gels provide good separation resolution at relatively low electric field strengths (10-20 V/cm). This makes it possible to customize the microfabricated electrophoresis chip for microdevice-based applications according to desired separation performance.

  11. Application of optical methods for dose evaluation in normoxic polyacrylamide gels irradiated at two different geometries

    NASA Astrophysics Data System (ADS)

    Adliene, D.; Jakstas, K.; Vaiciunaite, N.

    2014-03-01

    Normoxic gels are frequently used in clinical praxis for dose assessment or 3-D dose imaging in radiotherapy due to their relative simple manufacturing process under normal atmospheric conditions, spatial stability and well expressed modification feature of physical properties which is related to radiation induced polymerization of gels. In this work we have investigated radiation induced modification of the optical properties of home prepared normoxic polyacrylamide gels (nPAG) in relation to polymerization processes that occur in irradiated gels. Two irradiation geometries were used for irradiation of gel samples: broad beam irradiation geometry of teletherapy unit ROKUS-M with a 60Co source and point source irradiation geometry using 192Ir source of high dose rate afterloading brachytherapy unit MicroSelectron v2 which was inserted into gel via 6 Fr (2 mm thick) catheter. Verification of optical methods: UV-VIS spectrometry, spectrophotometry, Raman spectroscopy for dose assessment in irradiated gels has been performed. Aspects of their application for dose evaluation in gels irradiated using different geometries are discussed. Simple pixel-dose based photometry method also has been proposed and evaluated as a potential method for dose evaluation in catheter based interstitial high dose rate brachytherapy.

  12. Electrophoresis of proteins and protein-protein complexes in native polyacrylamide gels using a horizontal gel apparatus.

    PubMed

    Su, C; Wang, F; Ciolek, D; Pan, Y C

    1994-11-15

    Electrophoresis of proteins and protein-protein complexes in polyacrylamide gels under native conditions using a horizontal gel apparatus is described. The advantage of this system is that it permits the detection of both negatively and positively charged proteins as well as protein-protein complexes in the same gel. During electrophoresis, a continuous gel sandwiched between two glass plates is placed horizontally on the platform and submerged in a reservoir buffer. The sample wells are made along the center of the gel, allowing positively and negatively charged proteins to migrate toward the cathode and anode, respectively. Several proteins with varying molecular weights and isoelectric point (pI) values and pairs of proteins capable of forming protein-protein complexes were chosen as model systems to illustrate the methodology. The effects of several parameters on the performance of the gel system including protein molecular weight, pI, and gel concentration were also examined and the results obtained by this method are comparable to those obtained by the vertical system. Following electrophoresis, both negatively and positively charged proteins as well as protein-protein complexes can be transferred by electroblotting onto polyvinylidene difluoride membranes for further analyses. PMID:7695108

  13. Quantitation of specific proteins in polyacrylamide gels by the elution of Fast Green FCF.

    PubMed

    Gilmore, L B; Hook, G E

    1981-07-01

    The quantitation of proteins in polyacrylamide gels stained with Fast green FCF has been investigated using a modification of the elution technique originally described by Fenner et al. (Fenner, C., Traut, R.R., Mason, D.T. and Wikman-Coffelt, J. (1975) Anal. Biochem. 63, 595--602) for Coomassie Blue and adapted by Medugorac (Medugorac, I. (1979) Basic Res. Cardiol. 74, 406--416) for use with proteins stained with Fast Green FCF. The elution of dye from stained protein was accomplished using 1.0 M NaOH instead of aqueous pyridine as required by the original method. The primary advantages of our modification are that the time required for protein quantitation has been considerably reduced and the use of toxic organic solvents has been eliminated. We have investigated the applicability of the method of several different proteins and our results indicate: (a) The quantity of Fast Green FCF eluted from specific proteins is proportional to the quantity of protein applied to the gel, but varies for each individual protein. (b) The method allows quantitation over a very wide range of protein (1--800 micrograms). (c) Quantitation of protein is independent of the width of the stained bands as well as acrylamide concentration. (d) The method is applicable to gels of many types including disc, slab and continuous gradient gels. (e) Protein can be estimated from the patterns obtained by two-dimensional polyacrylamide gel electrophoresis. (f) The presence of Triton X-100 in gel and protein sample does not affect quantitation; the method is applicable to gels containing SDS provided that SDS is removed prior to staining. (g) Precipitation of protein with 12.5% TCA following electrophoresis does not interfere with quantitation. (h) The reproducibility of the technique is excellent, with standard deviations being less than 10% of the mean in all cases. This method appears highly versatile but requires appropriate standards for the quantitation of individual proteins. PMID:7276424

  14. Glutamine Synthetase Regulation, Adenylylation State, and Strain Specificity Analyzed by Polyacrylamide Gel Electrophoresis

    PubMed Central

    Bender, Robert A.; Streicher, Stanley L.

    1979-01-01

    We used polyacrylamide gel electrophoresis to examine the regulation and adenylylation states of glutamine synthetases (GSs) from Escherichia coli (GSE) and Klebsiella aerogenes (GSK). In gels containing sodium dodecyl sulfate (SDS), we found that GSK had a mobility which differed significantly from that of GSE. In addition, for both GSK and GSE, adenylylated subunits (GSK-adenosine 5′-monophosphate [AMP] and GSE-AMP) had lesser mobilities in SDS gels than did the corresponding non-adenylylated subunits. The order of mobilities was GSK-AMP < GSK < GSE-AMP < GSE. We were able to detect these mobility differences with purified and partially purified preparations of GS, crude cell extracts, and whole cell lysates. SDS gel electrophoresis thus provided a means of estimating the adenylylation state and the quantity of GS present independent of enzymatic activity measurements and of determining the strain origin. Using SDS gels, we showed that: (i) the constitutively produced GS in strains carrying the glnA4 allele was mostly adenylylated, (ii) the GS-like polypeptide produced by strains carrying the glnA51 allele was indistinguishable from wild-type GSK, and (iii) strains carrying the glnA10 allele contained no polypeptide having the mobility of GSK or GSK-AMP. Using native polyacrylamide gels, we detected the increased amount of dodecameric GS present in cells grown under nitrogen limitation compared with cells grown under conditions of nitrogen excess. In native gels there was neither a significant difference in the mobilities of adenylylated and non-adenylylated GSs nor a GS-like protein in cells carrying the glnA10 allele. Images PMID:33958

  15. Fractionation of heparin-derived oligosaccharides by gradient polyacrylamide-gel electrophoresis.

    PubMed Central

    Rice, K G; Rottink, M K; Linhardt, R J

    1987-01-01

    Heparin-derived oligosaccharides, prepared by using flavobacterial heparinase, having a high degree of heterogeneity (sequence variability) were resolved into sharp well-defined bands by using polyacrylamide gel electrophoresis (PAGE). The use of a stacking gel and a high-density-pore-gradient resolving gel was primarily responsible for the success of this separation. Low-Mr standards of known structure and having a degree of polymerization (dp) 2-6 were used to establish that the separation on gradient PAGE was primarily dependent on molecular size. High-Mr oligosaccharides (dp 8-20) were prepared using strong-anion-exchange h.p.l.c. and were used to help characterize the gradient PAGE separation. Kinetic profiles were obtained for the depolymerization of heparin and heparan sulphate with heparinase and heparitinase respectively. The utility of this approach in sequencing oligosaccharides derived from glycosaminoglycans is discussed. Images Fig. 3. Fig. 5. Fig. 7. PMID:3446173

  16. Oligosaccharide mapping of heparan sulphate by polyacrylamide-gradient-gel electrophoresis and electrotransfer to nylon membrane.

    PubMed Central

    Turnbull, J E; Gallagher, J T

    1988-01-01

    A new method that we have called 'oligosaccharide mapping' is described for the analysis of radiolabelled heparan sulphate and other glycosaminoglycans. The method involves specific enzymic or chemical scission of polysaccharide chains followed by high-resolution separation of the degradation products by polyacrylamide-gradient-gel electrophoresis. The separated oligosaccharides are immobilized on charged nylon membranes by electrotransfer and detected by fluorography. A complex pattern of discrete bands is observed covering an oligosaccharide size range from degree of polymerization (d.p.) 2 (disaccharide) to approximately d.p. 40. Separation is due principally to differences in Mr, though the method also seems to detect variations in conformation of oligosaccharide isomers. Resolution of oligosaccharides is superior to that obtained with isocratic polyacrylamide-gel-electrophoresis systems or gel chromatography, and reveals structural details that are not accessible by other methods. For example, in this paper we demonstrate a distinctive repeating doublet pattern of iduronate-rich oligosaccharides in heparitinase digests of mouse fibroblast heparan sulphate. This pattern may be a general feature of mammalian heparan sulphates. Oligosaccharide mapping should be a valuable method for the analysis of fine structure and sequence of heparan sulphate and other complex polysaccharides, and for making rapid assessments of the molecular distinctions between heparan sulphates from different sources. Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. Fig. 8. PMID:2969727

  17. Diffusion, Dispersion, and Mobility of Single-stranded DNA in Polyacrylamide Gel Electrophoresis

    NASA Astrophysics Data System (ADS)

    Lo, Roger; Ugaz, Victor

    2004-03-01

    The ability to perform DNA electrophoresis in miniaturized microfluidic systems has the potential to provide a new generation of low-cost high-throughput genomic analysis technology. Further progress toward improving separation performance under these conditions, however, requires a more detailed understanding of diffusion and dispersion phenomena in the gel matrix. Unfortunately, it has thus far proven difficult to obtain extensive measurements of these quantities due in large part to the lack of a convenient experimental platform. In this paper, we demonstrate the use of microfabricated gel electrophoresis devices to measure diffusion, dispersion, and mobility of single-stranded DNA fragments in crosslinked and uncrosslinked polyacrylamide gels. The microdevice format allows a complete set of diffusion and dispersion data to be collected in approximately one hour, as opposed to experiment times lasting several days using conventional sequencing equipment. By comparing runs using identical DNA samples, gel formulations, and operating conditions in both microfabricated electrophoresis devices and an ALF Express automated DNA sequencer, we are able to isolate the key factors governing separation performance in each system. The results of these experiments are then compared with biased reptation theory to extract information about the gel structure and predict achievable resolution. The effects of gel composition and polymerization chemistry are also explored.

  18. Differentiation of Campylobacter species by protein banding patterns in polyacrylamide slab gels.

    PubMed Central

    Ferguson, D A; Lambe, D W

    1984-01-01

    Soluble protein extracts of 37 catalase-positive strains of Campylobacter species were examined by polyacrylamide slab gel electrophoresis (PAGE). Electrophoretic banding patterns showed good correlation with biochemical tests and with available DNA homology data in distinguishing species of Campylobacter but did not differentiate subspecies or biotypes. PAGE patterns indicated that Campylobacter coli is a distinct species. Furthermore, the PAGE patterns indicated that C. jejuni and nalidixic acid-resistant thermophilic Campylobacter species (C. laridis) are each distinct species. The protein banding patterns of C. fetus subsp. venerealis and C. fetus subsp. fetus strains were distinctly different from those of the three thermophilic species. Images PMID:6490829

  19. 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.

  20. Human blood platelet membrane glycoproteins. Resolution in different polyacrylamide gel electrophoretic systems.

    PubMed

    Jenkins, C S; Ali-Briggs, E F; Zonneveld, G T; Sturk, A; Clemetson, K J

    1980-02-29

    The separation of the major platelet membrane glycoproteins of normal subjects and subjects with well defined platelet membrane glycoprotein abnormalities have been examined using four different polyacrylamide gel electrophoretic techniques (continuous and discontinuous). The mobilities of the resolved glycoprotein bands have been correlated with the glycoprotein nomenclature proposed for the conventional sodium dodecyl sulphate-phosphate buffer system. Since the glycoprotein distribution varies depending on the system used, the merits of each method should be considered before application to a specific problem. PMID:6768152

  1. High-resolution preparative separation of glycosaminoglycan oligosaccharides by polyacrylamide gel electrophoresis1

    PubMed Central

    Laremore, Tatiana N.; Ly, Mellisa; Solakyildirim, Kemal; Zagorevski, Dmitri V.; Linhardt, Robert J.

    2010-01-01

    Separation of milligram amounts of heparin oligosaccharides ranging in degree of polymerization from 4 to 32 is achieved within 6 hours using continuous-elution polyacrylamide gel electrophoresis (CE-PAGE) on commercially available equipment. The purity and structural integrity of CE-PAGE-separated oligosaccharides are confirmed by strong-anion exchange high-pressure liquid chromatography, electrospray ionization Fourier transform mass spectrometry and two-dimensional nuclear magnetic resonance spectroscopy. The described method is straightforward and time-efficient, affording size-homogeneous oligosaccharides that can be used in sequencing, protein binding, and other structure-function relationship studies. PMID:20211145

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

    SciTech Connect

    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 results from a commercial densitometer.

  3. 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

  4. High-throughput genotyping using horizontal polyacrylamide gels with wells arranged for microplate array diagonal gel electrophoresis (MADGE).

    PubMed

    Day, I N; Humphries, S E; Richards, S; Norton, D; Reid, M

    1995-11-01

    Genotyping (typing of genetic variation) typically involves PCR followed by an allele-specific oligonucleotide-binding assay, restriction enzyme digest or direct check of the outcome of a PCR designed to distinguish genotype. Electrophoresis can resolve "bound" from "free" oligonucleotide, as well as resolve PCR fragments and digests, but it is traditionally regarded as cumbersome and laborious in comparison with solution assays. Here we describe simple horizontal polyacrylamide gels which can receive a 96-well array of samples directly, which can be stacked in tanks and which are bound to a robust support of glass. The line of electrophoresis is on a 71.6 degree diagonal relative to the columns of the array (microplate array diagonal gel electrophoresis [MADGE]). Several thousand reactions can conveniently be analyzed in a shoebox-sized apparatus in a couple of hours. High resolution is achieved in the range of 20-1000 bp, information processing is simplified and automation is possible. PMID:8588924

  5. Partitioning and diffusion of proteins and linear polymers in polyacrylamide gels.

    PubMed Central

    Tong, J; Anderson, J L

    1996-01-01

    The equilibrium partition coefficient (K) and diffusion coefficient (Dgel) of two proteins and two linear polymers were measured as a function of polymer content of a 2.7% cross-linked polyacrylamide (PA) gel. The gel concentration, expressed as a volume percentage of PA in the gel (phi), varied between 0 and 14%. The measurements were made by fluorescence spectroscopy; fluorescent dyes were covalently attached to the macromolecules. The dependence of K on phi for the proteins agrees with a model of the gel network as randomly placed, impenetrable rods. The diffusion data are interpreted in terms of an effective medium theory for the mobility of a sphere in a Brinkman fluid. Using values of the Brinkman parameter in the literature, the effective medium model with no adjustable parameters fits the diffusion data for the proteins very well but underpredicts Dgel for the linear polymers. The gel effect on partitioning is significantly greater than that on diffusion. The permeability (KDgel) of bovine serum albumin decreased by 10(3) over the range phi = 0 --> 8%, and the ratio of permeabilities for ribonuclease compared to BSA increased from 2 to 30. Images FIGURE 1 PMID:8785307

  6. Improved dose sensitivity of normoxic polyacrylamide gelatin gel dosimeter with sucrose

    NASA Astrophysics Data System (ADS)

    Yoshioka, M.; Hayashi, S.; Usui, S.; Haneda, K.; Kondo, T.; Numasaki, H.; Teshima, T.; Tominaga, T.

    2010-11-01

    To improve the dose sensitivity of normoxic polyacrylamide gelatin gel (nPAG) dosimeter, the effect of sucrose as an additive is investigated. The dose-transverse relaxation rate (R2) characteristics of the samples of nPAG with different sucrose concentrations were examined, and temperature increases due to exothermic polymerization reaction in the irradiated gel were also measured. As the result, the dose-R2 sensitivity increased (~3 times) with increasing sucrose concentrations (0-25%), while other characteristics of dose response, such as dose integral property, dose rate dependence and temporal stability, were consistent with those of typical nPAG dosimeter. And as the sucrose concentrations increased, a larger temperature increase was observed. These results clearly indicate that the polymerization rate is increased with increasing sucrose concentrations.

  7. Reduction of Cr, Mo, Se and U by Desulfovibrio desulfuricans immobilized in polyacrylamide gels.

    PubMed

    Tucker, M D; Barton, L L; Thomson, B M

    1998-01-01

    Intact cells of Desulfovibrio desulfuricans, immobilized in polyacrylamide gel, removed Cr, Mo, Se and U from solution by enzymatic-mediated reduction reactions. Lactate or H2 served as the electron donor and the oxidized Cr(VI), Mo(VI), Se(VI) and U(VI) served as electron acceptors. Reduction of the oxidized metal species resulted in the precipitation of solid phases of the metals. Metal removal efficiencies of 86-96% were achieved for initial concentrations of 1 mM Mo, Se, and U and 0.5 mM Cr. Insoluble metal phases accumulated on both the surface and the interior of the polyacrylamide gel. In column tests conducted for U removal, effluent concentrations less than 20 micrograms L(-1) were achieved with initial concentrations of 5 mg L(-1) and 20 mg L(-1) U and residence times from 25-37 h. The enzymatic reduction of Cr, Mo, Se, and U by immobilized cells of D. desulfuricans may be a practical method for removing these metals from solution in a biological reactor. PMID:9565467

  8. Newcastle Disease Virus-Specific RNA: Polyacrylamide Gel Analysis of Single-Stranded RNA and Hybrid Duplexes

    PubMed Central

    Kaverin, Nicolai V.; Varich, Natalia L.

    1974-01-01

    Newcastle disease virus-specific [3H]uridine-labeled 18S RNA was resolved by polyacrylamide gel electrophoresis into several components with molecular weights from 450,000 to 840,000. The analysis of 35 and 24S virus-specific RNA also revealed several components in each sedimentational class. The conversion of 18S RNA into double-stranded form by hybridization with an excess of unlabeled virion RNA improved the resolution in polyacrylamide gels and revealed at least six distinct components. The same six classes of hybrid duplexes were revealed when 32P-labeled 50S virion RNA was hybridized with an excess of 18S RNA. The applicability of polyacrylamide gel electrophoresis of hybrid duplexes to the analysis of viral genome structure is discussed. PMID:4855736

  9. Model and field studies of the degradation of cross-linked polyacrylamide gels used during the revegetation of slate waste.

    PubMed

    Holliman, Peter J; Clark, Jennifer A; Williamson, Julie C; Jones, Davey L

    2005-01-01

    Cross-linked polyacrylamide gels are increasingly being used in environmental restoration schemes and horticulture as a means of enhancing water supply to plants. However, the environmental impact of cross-linked polyacrylamide gel deployment in soil remains poorly understood. This study assessed the chemical, physical and biological properties of new and field-conditioned cross-linked polyacrylamide gels. Both monomeric acrylamide (11 microg l(-1)) and acrylic acid (285 microg l(-1)) were observed in new gel; however, the levels of monomers in field-conditioned gels (1-6 years old) were very low (acrylamide <1 microg l(-1); acrylic acid <7 microg l(-1)). Generally, freeze-thaw processes and exposure to UV radiation had little effect on gel acrylic acid and acrylamide concentrations. However, elevated temperatures (35 degrees C) caused a significant release of up to 144 mug l(-1) of acrylamide and 453 microg l(-1) of acrylic acid in new gel and up to 25 microg l(-1) of acrylamide and 157 microg l(-1) of acrylic acid in field-conditioned gels. In contrast, gel water holding capacity was highly dependent upon environmental conditions (UV exposure and freeze/thaw cycles produced the greatest loss of water holding in new gels) and gel age. Optical microscopy revealed that after placement in the field the gels became increasingly colonised over time by fungi and bacteria. In enrichment cultures, we were unable, however, to demonstrate microbial growth when cross-linked polyacrylamide was used as the sole nitrogen source. In summary, under a range of conditions cross-linked polyacrylamide did not release acrylamide above legally permitted limits, with the exception of gel subjected to elevated temperatures. However, their capacity for holding water decreased sharply within 18 months. We therefore conclude that cross-linked polyacrylamide placed in soil is relatively stable with respect to the production of potentially toxic acrylamide, a species with a short half

  10. Separation performance of single-stranded DNA electrophoresis in photopolymerized cross-linked polyacrylamide gels.

    PubMed

    Lo, Roger C; Ugaz, Victor M

    2006-02-01

    Considerable effort has been directed toward optimizing performance and maximizing throughput in ssDNA electrophoresis because it is a critical analytical step in a variety of genomic assays. Ultimately, it would be desirable to quantitatively determine the achievable level of separation resolution directly from measurements of fundamental physical properties associated with the gel matrix rather than by the trial and error process often employed. Unfortunately, this predictive capability is currently lacking, due in large part to the need for a more detailed understanding of the fundamental parameters governing separation performance (mobility, diffusion, and dispersion). We seek to address this issue by systematically characterizing electrophoretic mobility, diffusion, and dispersion behavior of ssDNA fragments in the 70-1,000 base range in a photopolymerized cross-linked polyacrylamide matrix using a slab gel DNA sequencer. Data are collected for gel concentrations of 6, 9, and 12%T at electric fields ranging from 15 to 40 V/cm, and resolution predictions are compared with corresponding experimentally measured values. The data exhibit a transition from behavior consistent with the Ogston model for small fragments to behavior in agreement with the biased reptation model at larger fragment sizes. Mobility data are also used to estimate the mean gel pore size and compare the predictions of several models. PMID:16331587

  11. Blue native polyacrylamide gel electrophoresis (BN-PAGE) for analysis of multiprotein complexes from cellular lysates.

    PubMed

    Fiala, Gina J; Schamel, Wolfgang W A; Blumenthal, Britta

    2011-01-01

    Multiprotein complexes (MPCs) play a crucial role in cell signalling, since most proteins can be found in functional or regulatory complexes with other proteins (Sali, Glaeser et al. 2003). Thus, the study of protein-protein interaction networks requires the detailed characterization of MPCs to gain an integrative understanding of protein function and regulation. For identification and analysis, MPCs must be separated under native conditions. In this video, we describe the analysis of MPCs by blue native polyacrylamide gel electrophoresis (BN-PAGE). BN-PAGE is a technique that allows separation of MPCs in a native conformation with a higher resolution than offered by gel filtration or sucrose density ultracentrifugation, and is therefore useful to determine MPC size, composition, and relative abundance (Schägger and von Jagow 1991); (Schägger, Cramer et al. 1994). By this method, proteins are separated according to their hydrodynamic size and shape in a polyacrylamide matrix. Here, we demonstrate the analysis of MPCs of total cellular lysates, pointing out that lysate dialysis is the crucial step to make BN-PAGE applicable to these biological samples. Using a combination of first dimension BN- and second dimension SDS-PAGE, we show that MPCs separated by BN-PAGE can be further subdivided into their individual constituents by SDS-PAGE. Visualization of the MPC components upon gel separation is performed by standard immunoblotting. As an example for MPC analysis by BN-PAGE, we chose the well-characterized eukaryotic 19S, 20S, and 26S proteasomes. PMID:21403626

  12. Polyacrylamide Gel-Entrapped Maltase: An Excellent Design of Using Maltase in Continuous Industrial Processes.

    PubMed

    Nawaz, Muhammad Asif; Aman, Afsheen; Rehman, Haneef Ur; Bibi, Zainab; Ansari, Asma; Islam, Ziaul; Khan, Ishtiaq Ahmad; Qader, Shah Ali Ul

    2016-06-01

    Bacterial maltase catalyzes the hydrolysis of maltose and is known as one of the most significant hydrolases. It has several applications in different industrial processes but widely used in food fermentation technology and alcohol production. In the current study, entrapment technique was comprehensively examined using polyacrylamide gel as a matrix support to improve the stability and catalytic efficiency of maltase for continuous use. Maximum entrapment yield of maltase was achieved at 10 % polyacrylamide concentration with 3.0-mm bead size. Optimized conditions indicated an increase in the reaction temperature from 45 to 55 °C after maltase entrapment while no change was observed in the reaction time and pH. An increase in the K m value of entrapped maltase was attained whereas V max value decreased from 8411.0 to 6813.0 U ml(-1) min(-1) with reference to its free counterpart. Entrapped maltase showed remarkable thermal stability and retained 16 % activity at 70 °C even after 120.0 min. Entrapped maltase also exhibited excellent recycling efficiency up to eight consecutive reaction cycles. With respect to economic feasibility, entrapped maltase indicates its high potential to be used in various biotechnological applications. PMID:26847568

  13. Prestaining of glycoproteins in sodium dodecyl sulfate polyacrylamide gels by dansylhydrazine.

    PubMed

    Wang, Yang; Zhou, Xuan; Yu, Qing; Duan, Yuanmeng; Huang, Binbin; Hong, Guoying; Zhou, Ayi; Jin, Litai

    2014-06-01

    A new fluorescent prestaining method for gel-separated glycoproteins in 1D and 2D SDS-PAGE was developed by using dansylhydrazine in this study. The prestained gels could be easily imaged after electrophoresis without any time-consuming steps needed for poststains. As low as 4-8 ng glycoproteins (transferrin, α1-acid glycoprotein) could be selectively detected, which is comparable to that of Pro-Q Emerald 488, one of the most commonly used glycoprotein stain. In addition, a subsequent study of deglycosylation, glycoprotein affinity isolation, and LC-MS/MS analysis was performed to confirm the specificity of the newly developed method. PMID:24668852

  14. RegStatGel: proteomic software for identifying differentially expressed proteins based on 2D gel images

    PubMed Central

    Li, Feng; Seillier-Moiseiwitsch, Françoise

    2011-01-01

    Image analysis of two-dimensional gel electrophoresis is a key step in proteomic workflow for identifying proteins that change under different experimental conditions. Since there are usually large amount of proteins and variations shown in the gel images, the use of software for analysis of 2D gel images is inevitable. We developed open-source software with graphical user interface for differential analysis of 2D gel images. The user-friendly software, RegStatGel, contains fully automated as well as interactive procedures. It was developed and has been tested under Matlab 7.01. Availability The database is available for free at http://www.mediafire.com/FengLi/2DGelsoftware PMID:21904427

  15. Delayed gel indurations as an adverse effect of polyacrylamide filler and its easy treatment.

    PubMed

    Kavoussi, Hossein; Ebrahimi, Ali

    2012-01-01

    Background. The more increasing use of permanent soft tissue fillers such as polyacrylamide hydrogel (PAAG) for aesthetic purposes, the more adverse events resulting from them are reported. Occasionally, nonserious complications and misdiagnosis result in unnecessary surgeries and sequels. Objective. To introduce delayed gel indurations (DGIs) as a late onset complication of PAAG and its easy treatment. Patient and Methods. Twenty patients (17 females and 3 males) referred to us with subcutaneous mass at injected site of PAAG. We diagnosed DGI based on clinical and sonography findings and treatment was performed with a hole by 16-gauge needle and squeezing. Results. From 20 patients with 21 cases of DGI, 5 (23.8%), 5 (23.8%), and 5 (23.8%) cases in cheeks, glabella, and lips were seen, respectively. The time range between PAAG injection and presentation of patients was 10-28 months (mean = 17.5%). All of the patients responded very well to treatment without recurrence and any complications. Conclusion. DGI is a nonserious, late onset, and easily treated complication of PAAG that is probably induced due to water exchange between gel and surrounding tissue and modest host immune reaction to gel. PMID:23093956

  16. Migration of implants: a problem with injectable polyacrylamide gel in aesthetic plastic surgery.

    PubMed

    Cheng, Ning-xin; Xu, Shi-liang; Deng, Hui; Ding, Xiao-bang; Zhang, Xiao-man; Wu, Dai-hong; Zhong, Hong; Sun, Zi-hong

    2006-01-01

    Polyacrylamide gel (PAAG) has been used as a soft tissue filler material for cosmetic purposes in Europe and China since 1997. The various complications of PAAG have been reported. A total of 15 patients who received PAAG injections at other institutions were treated for gel migration in the authors' hospitals. During treatment, the authors found that the injected PAAG had not formed capsules within the muscle and was encapsulated only by thin fibrous tissue in skin and mammary glands. Consequently, the filler material migrated easily because of muscular activity or the influence of gravity, especially when the capsule was broken by incorrect massage or incidental force. It is suggested that PAAG should not be injected into muscular tissue or subcutaneous areas with active movement, such as joints and muscles involved in facial expression with thin skin. After years of gel implantation, the thinned capsule may result in an increasing incidence of this complication. Management and some clinical findings in relation to the complication also are discussed. PMID:16547628

  17. Delayed Gel Indurations as an Adverse Effect of Polyacrylamide Filler and Its Easy Treatment

    PubMed Central

    Kavoussi, Hossein; Ebrahimi, Ali

    2012-01-01

    Background. The more increasing use of permanent soft tissue fillers such as polyacrylamide hydrogel (PAAG) for aesthetic purposes, the more adverse events resulting from them are reported. Occasionally, nonserious complications and misdiagnosis result in unnecessary surgeries and sequels. Objective. To introduce delayed gel indurations (DGIs) as a late onset complication of PAAG and its easy treatment. Patient and Methods. Twenty patients (17 females and 3 males) referred to us with subcutaneous mass at injected site of PAAG. We diagnosed DGI based on clinical and sonography findings and treatment was performed with a hole by 16-gauge needle and squeezing. Results. From 20 patients with 21 cases of DGI, 5 (23.8%), 5 (23.8%), and 5 (23.8%) cases in cheeks, glabella, and lips were seen, respectively. The time range between PAAG injection and presentation of patients was 10–28 months (mean = 17.5%). All of the patients responded very well to treatment without recurrence and any complications. Conclusion. DGI is a nonserious, late onset, and easily treated complication of PAAG that is probably induced due to water exchange between gel and surrounding tissue and modest host immune reaction to gel. PMID:23093956

  18. Phosphoproteome profiling using a fluorescent phosphosensor dye in two-dimensional polyacrylamide gel electrophoresis.

    PubMed

    Otani, Mieko; Taniguchi, Taizo; Sakai, Akiko; Seta, Jouji; Kadoyama, Keiichi; Nakamura-Hirota, Tooru; Matsuyama, Shogo; Sano, Keiji; Takano, Masaoki

    2011-07-01

    We validated the novel PhosphoQUANTI SolidBlue Complex (PQSC) dye for the sensitive fluorescent detection of phosphorylated proteins in polyacrylamide- and two-dimensional gel electrophoresis (PAGE and 2DE, respectively). PQSC can detect as little as 15.6 ng of ß-casein, a pentaphosphorylated protein, and 61.3 ng of ovalbumin, a diphosphorylated protein. Fluorescence intensity correlates with the number of phosphorylated residues on the protein. To demonstrate the specificity of PQSC for phosphoproteins, enzymatically dephosphorylated lysates of Swiss 3T3 cells were separated in 2DE gels and stained by PQSC. The fluorescence signals in these gels were markedly reduced following dephosphorylation. When the phosphorylated proteins in Swiss 3T3 cell lysates were concentrated using a phosphoprotein enrichment column, the majority of phosphoproteins showed fluorescence signals in the pI 4-5 range. Finally, we performed phosphoproteome analysis to study differences in the protein phosphorylation profiles of proliferating and quiescent Swiss 3T3 cells. Over 135 discernible protein spots were detected, from which a selection of 15 spots were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF-MS). The PQSC staining procedure for phosphoprotein detection is simple, reversible, and fully compatible with MALDI TOF-MS. PMID:21384102

  19. Thermal stability of alpha-amylase from Aspergillus oryzae entrapped in polyacrylamide gel.

    PubMed

    Raviyan, Patcharin; Tang, Juming; Rasco, Barbara A

    2003-08-27

    To determine the suitability as a time-temperature indicator for dielectric pasteurization processes, the thermal stability (50-75 degrees C) of Aspergillus oryzae alpha-amylase immobilized in polyacrylamide gel in phosphate buffer, mashed potatoes, and minced shrimp was examined. Changing the cross-linking agent concentration from 3.3 to 5.3% and adding 2% salt did not markedly affect the thermal stability of the immobilized alpha-amylase. Thermal inactivation was first order, and immobilization generally improved the thermal stability of alpha-amylase. z values of the immobilized system in test food systems were 10.2 degrees C (phosphate buffer), 8.45 degrees C (minced shrimp), and 7.78 degrees C (mashed potatoes). PMID:12926898

  20. 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

  1. 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. PMID:22475746

  2. Characterization of the aerosol produced by infrared femtosecond laser ablation of polyacrylamide gels for the sensitive inductively coupled plasma mass spectrometry detection of selenoproteins

    NASA Astrophysics Data System (ADS)

    Claverie, Fanny; Pécheyran, Christophe; Mounicou, Sandra; Ballihaut, Guillaume; Fernandez, Beatriz; Alexis, Joël; Lobinski, Ryszard; Donard, Olivier F. X.

    2009-07-01

    A 2D high repetition rate femtosecond laser ablation strategy (2-mm wide lane) previously developed for the detection of selenoproteins in gel electrophoresis by inductively coupled plasma mass spectrometry was found to increase signal sensitivity by a factor of 40 compared to conventional nanosecond ablation (0.12-mm wide lane) [G. Ballihaut, F. Claverie, C. Pécheyran, S. Mounicou, R. Grimaud and R. Lobinski, Sensitive Detection of Selenoproteins in Gel Electrophoresis by High Repetition Rate Femtosecond Laser Ablation-Inductively Coupled Plasma Mass Spectrometry, Anal. Chem. 79 (2007) 6874-6880]. Such improvement couldn't be explained solely by the difference of amount of material ablated, and then, was attributed to the aerosol properties. In order to validate this hypothesis, the characterization of the aerosol produced by nanosecond and high repetition rate femtosecond laser ablation of polyacrylamide gels was investigated. Our 2D high repetition rate femtosecond laser ablation strategy of 2-mm wide lane was found to produce aerosols of similar particle size distribution compared to nanosecond laser ablation of 0.12-mm wide lane, with 38% mass of particles < 1 µm. However, at high repetition rate, when the ablated surface was reduced, the particle size distribution was shifted toward thinner particle diameter (up to 77% for a 0.12-mm wide lane at 285 µm depth). Meanwhile, scanning electron microscopy was employed to visualize the morphology of the aerosol. In the case of larger ablation, the fine particles ejected from the sample were found to form agglomerates due to higher ablation rate and then higher collision probability. Additionally, investigations of the plasma temperature changes during the ablation demonstrated that the introduction of such amount of polyacrylamide gel particles had very limited impact on the ICP source (Δ T~ 25 ± 5 K). This suggests that the cohesion forces between the thin particles composing these large aggregates were weak

  3. Studies on the bioactivity of radioiodinated highly purified bovine thyrotropin: analytical polyacrylamide gel electrophoresis

    SciTech Connect

    Takai, N.A.; Filetti, S.; Rapoport, B.

    1981-01-01

    Highly purified bovine TSH (stored in solution at -70 C) was radioiodinated by the stoichiometric chloroamine-T method. The iodinated material ws subjected to analytical polyacrylamide disc gel electrophoresis. TSH was eluted from gel slices (1 mm width) and was analyzed for radioactivity and bioactivity. The latter was determined using the cultured thyroid cell cAMP response assay. Radioactivity in the TSH preparation migrated separately from bioactivity, but concordant with the protein bands observed in gels run in parallel. Further studies performed on bovine TSH purified in our laboratory, as well as on a different TSH preparation of exceptionally high potency (both stored as lyophilized powder) revealed a different pattern, with TSH bioactivity and radioactivity eluting concurrently. Iodination of TSH did not alter its electrophoretic migration on disc gel electrophoresis. In all preparations polymorphism of TSH bioactivity was observed, with at least four separate protein bands containing TSH bioactivity being present in our preparation. The relationship between the degree of iodination and retention of TSH bioactivity was examined. Incorporation of /sup 125/I into TSH was greatly different at two different concentrations of chloramine-T. Despite this, however, the progressive loss of TSH bioactivity was similar at both concentrations, indicating that incorporation of iodine into the TSH molecule is not itself responsible for the decrease in bioactivity. These studies indicate variability among different TSH preparations in terms of their retention of bioactivity. Significant loss of TSH bioactivity appears to occur during storage in solution. The damage to the biological activity of TSH during the iodination procedure is more likely related to the oxidation process than to the incorporation of iodine.

  4. Imaging findings of breast augmentation with injected hydrophilic polyacrylamide gel: patient reports and literature review.

    PubMed

    Khedher, Najoua Ben; David, Julie; Trop, Isabelle; Drouin, Suzanne; Peloquin, Laurence; Lalonde, Lucie

    2011-04-01

    Hydrophilic polyacrylamide gel (PAAG) is a nonresorbable soft tissue filler that has been used as implant material for breast augmentation in some countries, particularly from the Asian continent. Many complications associated with hydrogel use have been reported in the clinical literature including inflammation, persistent mastodynia, formation of multiple lumps, poor cosmetic results, glandular atrophy, and significant spread of hydrogel into the surrounding tissue. Data on long-term toxicity is currently unavailable. The radiologic features of PAAG injection mammoplasty frequently constitute a diagnostic challenge for radiologists. Indeed, the imaging appearances of uncomplicated PAAG implants may mimic conventional implants on mammography, sonography and MRI, with some distinguishing features. The location and local spread of the injected PAAG, and the eventual detection of local inflammation, are best evaluated by ultrasonography and especially MRI, considered the most sensitive technique for assessment of PAAG mammoplasty. MRI clearly depicts the volume and the distribution of gel within the breast; contrast medium enhancement allows delineation of areas of inflammation and infection. It is important to be familiar with the spectrum of imaging findings in order to make an accurate diagnosis and offer proper management. This paper aims to review the normal and abnormal mammographic, sonographic, and MR imaging characteristics of PAAG augmentation mammoplasty through presented patient reviews of three women having undergone direct PAAG injection. PMID:19836915

  5. 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

  6. Alkaline phosphatase isoenzymes in mouse plasma detected by polyacrylamide-gel disk electrophoresis.

    PubMed

    Hatayama, Kazuhisa; Nishihara, Yoshito; Kimura, Sayaka; Goto, Ken; Nakamura, Daichi; Wakita, Atsushi; Urasoko, Yoshinaka

    2011-04-01

    Plasma alkaline phosphatase (ALP) activity is frequently measured in toxicity studies. In the present study, we assessed the usefulness of a commercially available polyacrylamide-gel (PAG) disk electrophoresis kit used in humans (AlkPhor System, Jokoh Co., Ltd., Tokyo, Japan) for identifying plasma ALP isoenzymes in mice of the Crlj:CD1 strain (ICR mice), which are commonly used in toxicity studies. We also examined age-related changes in plasma ALP isoenzymes in ICR mice. Electrophoresis was performed according to the manufacturer's instructions. In order to identify the origin of each ALP isoenzyme, in addition to plasma samples, tissue ALP extracts from the liver, bone and small intestine were treated with neuraminidase, anti-small intestinal ALP antibody, ALP inhibitor levamisole and/or wheat germ agglutinin (WGA). The kit revealed that main plasma ALP isoenzyme in intact ICR mice was bone-derived one, and it tended to decrease with age. On the other hand, liver-derived ALP isoenzyme greatly increased in plasma of cholestasis model mice induced by bile duct ligation. This model mouse had also a large molecular ALP detected in the stacking gel. This ALP was thought to be of intestinal origin because its activity remained even after levamisole inhibition. In addition, a minimum sample volume for sufficient resolution of plasma ALP isoenzymes was only 14µl. The results of this study suggest that the present method is a useful tool for detecting plasma ALP isoenzymes in mice and that pre-treatment of plasma with neuraminidase and concomitant levamisole inhibition with another gel is applicable for the evaluation of organ toxicity. PMID:21467748

  7. Is gravity on our way? The case of polyacrylamide gel polymerization.

    PubMed

    Righetti, P G; Bossi, A; Giglio, M; Vailati, A; Lyubimova, T; Briskman, V A

    1994-01-01

    Potential gravity-induced deformations of polyacrylamide matrices during gelling were investigated in two different initiator systems based on (i) photopolymerization with 100 microM methylene blue, 1 mM sodium toluene sulfinate (reducer) and 50 microM diphenyliodonium chloride (oxidizer) (photopolymerization) and (ii) chemical polymerization, utilizing the standard persulfate N,N,N',N'-tetramethylethylenediamine. In both systems, it is seen that convective flows are imprinted in the final gel structure above a critical gelling layer thickness, set at ca. 3 mm. In both systems, progressive increments of the solution density, from normodense (density = 1.0) up to isodense with the growing polymer chains (density = 1.3) do not inhibit the appearance of strong convective flows. However, gel inhomogeneities are completely abolished even in 10 mm gelling layers if polymerization is performed in presence of density gradients, notably of sucrose, from 0 to 20%, 0 to 40% and 0 to 60%. Even the shallower gradient (0-20% sucrose) is able to completely abolish convective flows in persulfate-driven polymerization. It is hypothesized that such disturbances are not created by sedimentation of the growing polymer chains in the gravitational field, but are produced by the reaction exothermality, which produces strong buoyancy-driven flows. It is additionally demonstrated that persulfate polymerization is sensitive to oxygen absorbed from the top liquid layers, which should be carefully protected by an overlay of organic solvent. Methylene blue-induced polymerization appears to offer a series of unique advantages over chemical initiation with persulfate. PMID:7859700

  8. Late hematoma, seroma, and galactocele in breasts injected with polyacrylamide gel.

    PubMed

    Cheng, Ning-Xin; Zhang, Yuan-Long; Luo, Sheng-Kang; Zhang, Xiao-Man; Hui, Li; Chen, Yuan-Liang; Sheng, Shao-Yong; Wu, Dai-Hong; Wang, Hai-Bin; Li, Ping

    2011-06-01

    Late hematoma or seroma and galactocele caused by augmentation mammaplasty have been reported in patients with silicon breast prostheses but are extremely rare in patients injected with polyacrylamide gel (PAAG). In a retrospective survey, the incidence, clinical manifestations, and management of late hematoma, seroma, and galactocele in 28 of 2,610 patients who underwent breast augmentation with PAAG injection were investigated, and 5 typical cases are presented. The diagnostic and managing methods for this complication have been assessed. The incidence of late hematoma or seroma was 0.65% and that of galactocele was 0.35% among patients with PAAG-injected breast augmentations. The clinical onsets of such late PAAG complications were of two types: rapid enlargement in 17 patients and progressive expansion in another 11 patients. Aspiration, ultrasound, and magnetic resonance imaging (MRI) are useful and sensitive tools for diagnosis. Foreign body reaction, PAAG-related tissue necrosis and fibrosis, and granuloma were shown, and the bacterial cultures in all 12 cases were negative. Needle aspiration with pressure dressing has been advocated as a reliable method for small diseases, and surgical exploration with irrigation-vacuum drainage and evacuation with capsulectomy have been considered more effective for recurrent, large, and long-term cases. In conclusion, these late complications rarely present after large-volume injections of PAAG for breast augmentation. The PAAG-related pathologic inflammatory tissue changes are suggested as the pathogenesis for the complication. Trauma and breastfeeding are considered to be stimulating factors. PMID:21072516

  9. [Studies on human alpha-2 macroglobulin structure and its complexes with proteases, using polyacrylamide gel electrophoresis].

    PubMed

    Fine, J M; Lambin, P; Steinbuch, M

    1975-09-01

    Pure alpha2M is prepared with fresh plasma as starting material, to prevent the interaction of alpha2M from proteolytic enzymes of plasma such as thrombin, plasmin and kallikrein. During the purification steps, polybrene and aprotin are used as inhibitors and plasminogen is absorbed onto bentonite. When alpha 2M is submitted to polyacrylamide gel electrophoresis (PAA) containing 0.1% SDS, a complete dissociation in two half-molecules of MW 380,000 occurs. When alpha2M is incubated in 1% SDS and 1% beta-mercaptoethanol as reducing agent, only one component of MW 190,000 is observed in PAA-SDS. This experiments show that the alpha2M molecule consist of two symetric halves of same MW (380,000) linked by non covalent bonds. Each two-half-molecules is made of two polypeptides chains MW 190,000 linked by disulfide bonds. Thus alpha2M molecule contains four polypeptides chains having a same MW. The same techniques were applied to the study of alaph2M proteinases complexes. Three different proteinases (plasmin, trypsin and papain) were used in these experiments. Trypsin and papain are commercialy available. Plasminogen was obtained by affinity chromatography and activated into plasmin by insoluble streptokinase fixed on PAB cellulose. PMID:59941

  10. Mechanosensitivity of astrocytes on optimized polyacrylamide gels analyzed by quantitative morphometry

    NASA Astrophysics Data System (ADS)

    Moshayedi, Pouria; Costa, Luciano da F.; Christ, Andreas; Lacour, Stephanie P.; Fawcett, James; Guck, Jochen; Franze, Kristian

    2010-05-01

    Cells are able to detect and respond to mechanical cues from their environment. Previous studies have investigated this mechanosensitivity on various cell types, including neural cells such as astrocytes. In this study, we have carefully optimized polyacrylamide gels, commonly used as compliant growth substrates, considering their homogeneity in surface topography, mechanical properties, and coating density, and identified several potential pitfalls for the purpose of mechanosensitivity studies. The resulting astrocyte response to growth on substrates with shear storage moduli of G' = 100 Pa and G' = 10 kPa was then evaluated as a function of coating density of poly-D-lysine using quantitative morphometric analysis. Astrocytes cultured on stiff substrates showed significantly increased perimeter, area, diameter, elongation, number of extremities and overall complexity if compared to those cultured on compliant substrates. A statistically significant difference in the overall morphological score was confirmed with an artificial intelligence-based shape analysis. The dependence of the cells' morphology on PDL coating density seemed to be weak compared to the effect of the substrate stiffness and was slightly biphasic, with a maximum at 10-100 µg ml - 1 PDL concentration. Our finding suggests that the compliance of the surrounding tissue in vivo may influence astrocyte morphology and behavior.

  11. Microscopic agglutination and polyacrylamide gel electrophoresis analyses of oral anaerobic spirochetes.

    PubMed Central

    Tall, B D; Nauman, R K

    1986-01-01

    Microscopic agglutination (MA) analysis and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were used to determine strain and species similarities and dissimilarities among three species of oral anaerobic spirochetes, Treponema denticola, Treponema pectinovorum, and Treponema vincentii. The MA analysis revealed a diversity of serologic reactivity or sharing of common antigens within each species. However, there was no cross-reactivity or sharing of common antigens among the three species. Distinct SDS-PAGE whole-cell electrophoretograms for each species were obtained. The banding patterns for 16 T. denticola strains revealed 30 distinct proteins, while the banding patterns for 5 strains of T. pectinovorum and 2 strains of T. vincentii revealed 26 and 35 distinct proteins, respectively. Analysis of the electrophoretograms showed that their respective banding patterns could be used to distinguish the three species from one another. In addition, strain differences within each species could be detected. There was a correlation between MA analysis and SDS-PAGE analysis. It is thus suggested that both MA and SDS-PAGE analysis be included in classification schemes for the identification of oral spirochetes. Images PMID:3745424

  12. Mechanosensitivity of astrocytes on optimized polyacrylamide gels analyzed by quantitative morphometry.

    PubMed

    Moshayedi, Pouria; Costa, Luciano da F; Christ, Andreas; Lacour, Stephanie P; Fawcett, James; Guck, Jochen; Franze, Kristian

    2010-05-19

    Cells are able to detect and respond to mechanical cues from their environment. Previous studies have investigated this mechanosensitivity on various cell types, including neural cells such as astrocytes. In this study, we have carefully optimized polyacrylamide gels, commonly used as compliant growth substrates, considering their homogeneity in surface topography, mechanical properties, and coating density, and identified several potential pitfalls for the purpose of mechanosensitivity studies. The resulting astrocyte response to growth on substrates with shear storage moduli of G' = 100 Pa and G' = 10 kPa was then evaluated as a function of coating density of poly-D-lysine using quantitative morphometric analysis. Astrocytes cultured on stiff substrates showed significantly increased perimeter, area, diameter, elongation, number of extremities and overall complexity if compared to those cultured on compliant substrates. A statistically significant difference in the overall morphological score was confirmed with an artificial intelligence-based shape analysis. The dependence of the cells' morphology on PDL coating density seemed to be weak compared to the effect of the substrate stiffness and was slightly biphasic, with a maximum at 10-100 µg ml(-1) PDL concentration. Our finding suggests that the compliance of the surrounding tissue in vivo may influence astrocyte morphology and behavior. PMID:21386440

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

    PubMed Central

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

    2015-01-01

    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. PMID:26203364

  14. Proteomic analysis of melanoma-derived exosomes by two-dimensional polyacrylamide gel electrophoresis and mass spectrometry.

    PubMed

    Mears, Rainy; Craven, Rachel A; Hanrahan, Sarah; Totty, Nick; Upton, Carol; Young, Sarah L; Patel, Poulam; Selby, Peter J; Banks, Rosamonde E

    2004-12-01

    Exosomes are 40-100 nm vesicles released by numerous cell types and are thought to have a variety of roles depending on their origin. Exosomes derived from antigen presenting cells have been shown to be capable of initiating immune responses in vivo and eradicating established tumours in murine models. Tumour-derived exosomes can be utilised as a source of tumour antigen for cross-priming to T-cells and are thus of interest for use in anti-tumour immunotherapy. Further exploration into the protein composition of exosomes may increase our understanding of their potential roles in vivo and this study has examined the proteome of exosomes purified from cell supernatants of the melanoma cell lines MeWo and SK-MEL-28. The vesicular nature and size (30-100 nm) of the purified exosomes was confirmed by electron microscopy and sucrose density gradient centrifugation. Western blotting demonstrated the absence of calnexin and cytochrome c, verifying the purity of the exosome preparations, as well as enrichment of MHC class I and the tumour-associated antigens Mart-1 and Mel-CAM. The two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) protein profiles of exosomes from the two cell lines were highly comparable and strikingly different from the profiles of the total cell lysates. Mass spectrometric sequencing identified proteins present in 49 protein spots in the exosome lysates. Several of these have been identified previously in exosomes but some are novel, including p120 catenin, radixin, and immunoglobulin superfamily member 8 (PGRL). Proteins present in whole-cell lysates that were significantly reduced or excluded from exosomes were also identified and included several mitochondrial and lysosomal proteins, again confirming the proposed endosomal origin of exosomes. This study presents a starting point for future more in-depth protein studies of tumour-derived exosomes which will aid the understanding of their biogenesis and targeting for use in anti

  15. Method for the typing of Clostridium difficile based on polyacrylamide gel electrophoresis of (/sup 35/S)methionine-labeled proteins

    SciTech Connect

    Tabaqchali, S.; O'Farrell, S.; Holland, D.; Silman, R.

    1986-01-01

    A typing method for Clostridium difficile based on the incorporation of (/sup 35/S)methionine into cellular proteins, their separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and their visualization by autoradiography is described. On analysis of the radiolabeled-protein profiles, nine distinct groups were observed (A to E and W to Z). The method, which is simple, reproducible, and readily expandable, has been applied in epidemiological studies to demonstrate cross-infection and hospital acquisition of C. difficile.

  16. The monitoring of nucleotide diphosphate kinase activity by blue native polyacrylamide gel electrophoresis.

    PubMed

    Mailloux, Ryan J; Darwich, Rami; Lemire, Joseph; Appanna, Vasu

    2008-04-01

    Nucleoside diphosphate kinase (NDPK) has been shown to play a pivotal role in modulating a plethora of cellular processes. In this study, we report on a blue native (BN) PAGE technique which allows the facile assessment of NDPK activity and expression. The in-gel detection of NDPK relies on the precipitation of formazan at the site of immobilized enzyme activity. This is achieved by coupling the formation of ATP, as a consequence of gamma-phosphate transfer from NTP to ADP, to hexokinase (HK), glucose-6-phosphate dehydrogenase (G6PDH), oxidized nicotinamide adenine dinucleotide phosphate (NADP), phenazine methosulfate (PMS), and iodonitrotetrazolium chloride (INT). 2-D denaturing gel analysis confirmed that the activity bands corresponded to NDPK as indicated by subunit composition. Furthermore, the sensitivity and specificity of this readily accessible procedure was assessed by monitoring the in-gel activity of NDPK using different concentrations of GTP and CTP as well as deoxynucleoside triphosphates. This electrophoretic technique allows the quick and easy detection of NDPK, a housekeeping enzyme crucial to cell survival. PMID:18324728

  17. 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. PMID:21601917

  18. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of urinary protein in acute kidney injury.

    PubMed

    Suhail, Sufi M; Woo, K T; Tan, H K; Wong, K S

    2011-07-01

    Recent experimental and clinical studies have shown the importance of urinary proteomics in acute kidney injury (AKI). We analyzed the protein in urine of patients with clinical AKI using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) for its diagnostic value, and followed them up for 40 months to evaluate prognosis. Urine from 31 consecutive cases of AKI was analyzed with SDS-PAGE to determine the low, middle and high molecular weight proteins. Fractional excretion of sodium (FENa) was estimated from serum and urine creatinine and sodium (Na). The cases were followed-up for 40 months from the end of the recruitment of study cases. Glomerular protein was higher in the hematuria group when compared with the non-hematuria group (P <0.04) and in the AKI group than in the acute on chronic renal failure (AKI-on-CRF) group (P <0.002). Tubular protein was higher in the AKI-on-CRF group (P <0.003) than in the AKI group. Tubular protein correlated with FENa in groups with diabetes mellitus (DM), AKI-on-CRF, and without hematuria (P <0.03, P <0.02 and P <0.004, respectively). Pattern of protein did not differ between groups with and without DM and clinical acute tubular necrosis (ATN). At the end of 40 months follow-up, category with predominantly glomerular protein progressed to chronic renal failure (CRF) or end-stage renal failure in higher proportion (P <0.05). In clinical AKI, we observed that glomerular protein dominated in cases with glomerular insult, as indicated by hematuria. Tubular protein was common in the study cases with CRF, DM and cases without hematuria. This indicates tubulo-interstitial injury for AKI in these cases. Patients with predominantly glomerular protein had an adverse outcome. PMID:21743220

  19. Detection of antimicrobial (poly)peptides with acid urea polyacrylamide gel electrophoresis followed by Western immunoblot.

    PubMed

    Porter, Edith; Valore, Erika V; Anouseyan, Rabin; Salzman, Nita H

    2015-01-01

    Antimicrobial (poly)peptides (AMPs) are ancient key effector molecules of innate host defense and have been identified in mammals, insects, plants, and even fungi (Nakatsuji and Gallo, J Invest Dermatol, 132: 887-895, 2012). They exhibit a cationic net charge at physiological pH and are rich in hydrophobic amino acids (Dufourc et al., Curr Protein Pept Sci, 13: 620-631, 2012). Their mode of action has been best investigated in bacteria. When assuming secondary structure the cationic and hydrophobic amino acids are sequestered creating a bipartitioned molecule in which the cationic amino acids mediate initial electrostatic interaction with the negatively charged bacterial surface and the hydrophobic amino acids mediate embedding into the bacterial membranes followed by a multitude of effects interfering with bacterial viability (Nicolas, FEBS J, 276: 6483-6496, 2009; Padovan et al., Curr Protein Pept Sci, 11: 210-219, 2010). However, immunomodulatory, antitumor, and other effects have been added to the ever increasing list of AMP functions (Pushpanathan et al., Int J Pept, 2013: 675391, 2013). Several classes of AMPs have been distinguished based on structure, namely anti-parallel beta-sheet, alpha-helical, circular, as well as disulfide bridge connectivity (Bond and Khalid, Protein Pept Lett, 17: 1313-1327, 2010). Many of the AMPs undergo posttranslational modification including further proteolysis. Biochemical analysis at the protein level is of great interest for a wide range of scientists and important when studying host-pathogen interaction, for example Salmonella invasion of the small intestine. Acid-urea polyacrylamide gel electrophoresis (AU-PAGE) followed by Western immunoblotting is an important tool for the identification and quantification of cationic AMPs. The protocol for these procedures outlined here describes, in detail, the necessary steps; including pouring the AU-gels, preparing the test samples, performing the electrophoretic separation and

  20. Development of an integrated approach for evaluation of 2-D gel image analysis: Impact of multiple proteins in single spots on comparative proteomics in conventional 2-D gel/MALDI workflow

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With 2-D gel mapping, it is often observed that essentially identical proteins migrate to different positions in the gel, while some seemingly well-resolved protein spots consist of multiple proteins. These observations can undermine the validity of gel-based comparative proteomic studies. Through...

  1. Multifunctional graphene incorporated polyacrylamide conducting gel electrolytes for efficient quasi-solid-state quantum dot-sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Duan, Jialong; Tang, Qunwei; Li, Ru; He, Benlin; Yu, Liangmin; Yang, Peizhi

    2015-06-01

    Pursuit of a high efficiency and stability has been a persistent objective for quantum dot-sensitized solar cells (QDSCs). Here we launch a strategy of synthesizing graphene implanted polyacrylamide (PAAm-G) conducting gel electrolytes for quasi-solid-state QDSCs. With an aim of elevating the dosage of S2-/Sx2- redox couples and therefore charge-transfer ability, both osmotic press across the PAAm-G and capillary force within the three-dimensional micropores are utilized as driving forces. A promising power conversion efficiency of 2.34% is recorded for the QDSCs by optimizing graphene dosage in the conducting gel electrolyte. The enhanced conversion efficiency of solar cell is attributed to the expanded catalytic area from counter electrolyte/electrolyte interface to both interface and the conducting gel electrolyte.

  2. Macroscopic observations of molecular recognition: discrimination of the substituted position on the naphthyl group by polyacrylamide gel modified with β-cyclodextrin.

    PubMed

    Zheng, Yongtai; Hashidzume, Akihito; Takashima, Yoshinori; Yamaguchi, Hiroyasu; Harada, Akira

    2011-11-15

    Macroscopic molecular recognition observations were realized using polyacrylamide-based gels modified with α-cyclodextrin (α-CD), β-cyclodextrin (β-CD), 1-naphthylmethyl (1Np), and 2-naphthylmethyl (2Np) moieties, which are denoted as αCD(x)-gel, βCD(x)-gel, 1Np(y)-gel, and 2Np(y)-gel, where x and y indicate the mol % of CD and Np moieties, respectively. The αCD(5)-gel did not adhere to either the 1Np(5)-gel or 2Np(5)-gel, whereas the βCD(5)-gel interacted with both to form alternating or checkered assemblies. Although the difference in the association constants of β-CD for the model polymers was small, the βCD(x)-gel successfully discriminated between 1Np(y)-gel and 2Np(y)-gel at the appropriate x and y. PMID:21978319

  3. High performance CCD camera system for digitalisation of 2D DIGE gels.

    PubMed

    Strijkstra, Annemieke; Trautwein, Kathleen; Roesler, Stefan; Feenders, Christoph; Danzer, Daniel; Riemenschneider, Udo; Blasius, Bernd; Rabus, Ralf

    2016-07-01

    An essential step in 2D DIGE-based analysis of differential proteome profiles is the accurate and sensitive digitalisation of 2D DIGE gels. The performance progress of commercially available charge-coupled device (CCD) camera-based systems combined with light emitting diodes (LED) opens up a new possibility for this type of digitalisation. Here, we assessed the performance of a CCD camera system (Intas Advanced 2D Imager) as alternative to a traditionally employed, high-end laser scanner system (Typhoon 9400) for digitalisation of differential protein profiles from three different environmental bacteria. Overall, the performance of the CCD camera system was comparable to the laser scanner, as evident from very similar protein abundance changes (irrespective of spot position and volume), as well as from linear range and limit of detection. PMID:27252121

  4. Nanopore density effect of polyacrylamide gel plug on electrokinetic ion enrichment in a micro-nanofluidic chip

    NASA Astrophysics Data System (ADS)

    Wang, Jun-yao; Xu, Zheng; Li, Yong-kui; Liu, Chong; Liu, Jun-shan; Chen, Li; Du, Li-qun; Wang, Li-ding

    2013-07-01

    In this paper, the nanopore density effect on ion enrichment is quantitatively described with the ratio between electrophoresis flux and electroosmotic flow flux based on the Poisson-Nernst-Planck equations. A polyacrylamide gel plug is integrated into a microchannel to form a micro-nanofluidic chip. With the chip, electrokinetic ion enrichment is relatively stable and enrichment ratio of fluorescein isothiocyanate can increase to 600-fold within 120 s at the electric voltage of 300 V. Both theoretical research and experiments show that enrichment ratio can be improved through increasing nanopore density. The result will be beneficial to the design of micro-nanofluidic chips.

  5. Isoelectric focusing of human parotid salivary proteins in hybrid carrier ampholyte-immobilized pH gradient polyacrylamide gels.

    PubMed

    Khoo, K S; Beeley, J A

    1990-06-01

    Isoelectric focusing of human salivary proteins with carrier ampholyte-isoelectric focusing systems requires prior desalting and concentration of samples, a procedure which is time-consuming and requires relatively large volumes of samples. By contrast, immobilized pH gradient gels are more tolerant to salt loads. Thus pretreatment of samples consists only of centrifugation prior to isoelectric focusing. If larger loads (greater than 50 micrograms) are required, the samples may be concentrated by lyophilization and reconstitution in a smaller volume of water or by dialysis against 30% w/v polyethylene glycol. Immobilized pH gradient polyacrylamide gels (incorporating a hybrid carrier ampholyte system) of two pH ranges (pH 4-9 and pH 3.5-5.0) have been used to separate the proteins in human parotid saliva. The effects of urea on focused patterns were studied; in pH 4-9 gels it gave improved resolution of protein bands, whereas in pH 3.5-5.0 gels it prevented protein precipitation. The salivary proteins were then visualized by staining with Coomassie Brilliant Blue G-250 or a silver procedure. Using the latter, 25-30 well-resolved bands were formed on a pH 4-9 gel loaded with 20 micrograms of proteins. The method offers considerable advantages compared with carrier ampholyte-isoelectric focusing. PMID:1697536

  6. Simultaneous electrophoretic analysis of proteins of very high and low molecular mass using Tris-acetate polyacrylamide gels.

    PubMed

    Cubillos-Rojas, Monica; Amair-Pinedo, Fabiola; Tato, Irantzu; Bartrons, Ramon; Ventura, Francesc; Rosa, Jose Luis

    2010-04-01

    To separate and analyze giant and small proteins in the same electrophoresis gel, we have used a 3-15% polyacrylamide gradient gel containing 2.6% of the crosslinker bisacrylamide and 0.2 M of Tris-acetate buffer (pH 7.0). Samples were prepared in a sample buffer containing lithium dodecyl sulphate and were run in the gel described above using Tris-Tricine-SDS-sodium bisulfite buffer, pH 8.2, as electrophoresis buffer. Here, we show that this system can be successfully used for general applications of SDS-PAGE such as CBB staining and immunoblot. Thus, by using Tris-acetate 3-15% polyacrylamide gels, it is possible to simultaneously analyze proteins, in the mass range of 10-500 kDa, such as HERC1 (532 kDa), HERC2 (528 kDa), mTOR (289 kDa), Clathrin heavy chain (192 kDa), RSK (90 kDa), S6K (70 kDa), beta-actin (42 kDa), Ran (24 kDa) and LC3 (18 kDa). This system is highly sensitive since it allows detection from as low as 10 microg of total protein per lane. Moreover, it has a good resolution, low cost, high reproducibility and allows for analysis of proteins in a wide range of weights within a short period of time. All these features together with the use of a standard electrophoresis apparatus make the Tris-acetate-PAGE system a very helpful tool for protein analysis. PMID:20309890

  7. Mutation analysis of fragile X syndrome by Southern blot, radioactive PCR, silver-stained polyacrylamide gel and DIG DNA

    SciTech Connect

    Lee, Sook-Hwan; Kim, Un-Kyung; Chung-Woong, M.S.

    1994-09-01

    Fragile X syndrome is the most common inherited form of mental retardation. In fragile X syndrome, the underlying mutation is caused by an expansion of the CTG triplet in the 5{prime} untranslated region of the FMR-1 gene located at Xq27.3 and diagnosed by methylation of the associated CpG island. This disorder becomes clinically manifested when the mutation is caused by an expansion of (CGG)n reaching a threshold of about 600bp (200 repeats). The number of inserted repeats increases through the generation. We have analyzed fragile X syndrome by 4 different methods: Southern blot, radioactive PCR, polyacrylamide gel and DIG DNA labeling/detection techniques. Southern blot and DIG DNA labeling/detection by double DNA digestion with EcoRI and EagI reveals both the presence of the mutation and the methylation status. Radioactive PCR and silver-stained polyacrylamide gel is a rapid and sensitive technique to define the unaffected carriers and NTMs, but it is difficult to amplify such a highly GC-rich sequence. Further testing in other fragile X patients is currently in progress.

  8. Total Protein Extraction and 2-D Gel Electrophoresis Methods for Burkholderia Species

    PubMed Central

    Velapatiño, Billie; Zlosnik, James E. A.; Hird, Trevor J.; Speert, David P.

    2013-01-01

    The investigation of the intracellular protein levels of bacterial species is of importance to understanding the pathogenic mechanisms of diseases caused by these organisms. Here we describe a procedure for protein extraction from Burkholderia species based on mechanical lysis using glass beads in the presence of ethylenediamine tetraacetic acid and phenylmethylsulfonyl fluoride in phosphate buffered saline. This method can be used for different Burkholderia species, for different growth conditions, and it is likely suitable for the use in proteomic studies of other bacteria. Following protein extraction, a two-dimensional (2-D) gel electrophoresis proteomic technique is described to study global changes in the proteomes of these organisms. This method consists of the separation of proteins according to their isoelectric point by isoelectric focusing in the first dimension, followed by separation on the basis of molecular weight by acrylamide gel electrophoresis in the second dimension. Visualization of separated proteins is carried out by silver staining. PMID:24192802

  9. Apolipoprotein distribution in human lipoproteins separated by polyacrylamide gradient gel electrophoresis.

    PubMed

    Vézina, C A; Milne, R W; Weech, P K; Marcel, Y L

    1988-05-01

    The heterogeneity of serum lipoproteins (excluding very low density (VLDL) and intermediate density (IDL) lipoproteins) and that of lipoproteins secreted by HepG2 cells has been studied by immunoblot analysis of the apolipoprotein composition of the particles separated by polyacrylamide gradient gel electrophoresis (GGE) under nondenaturing conditions. The reactions of antibodies to apoA-I, apoA-II, apoE, apoB, apoD, and apoA-IV have revealed discrete bands of particles which differ widely in size and apolipoprotein composition. GGE of native serum lipoproteins demonstrated that apoA-II is present in lipoproteins of limited size heterogeneity (apparent molecular mass 345,000 to 305,000) and that apoB is present in low density lipoproteins (LDL) and absent from all smaller or denser lipoproteins. In contrast, serum apoA-I, E, D, and A-IV are present in very heterogeneous particles. Serum apoA-I is present mainly in particles of 305 to 130 kDa where it is associated with apoA-II, and in decreasing order of immunoreactivity in particles of 130-90 kDa, 56 kDa, 815-345 kDa, and finally within the size range of LDL, all regions where there is little detectable apoA-II. Serum apoE is present in three defined fractions, one within the size range of LDL, one containing heterogeneous particles between 640 and 345 kDa, and one defined fraction at 96 kDa. Serum apoD is also present in three defined fractions, one comigrating with LDL, one containing heterogeneous particles between 390 and 150 kDa, and one band on the migration front. Most of serum apoA-IV is contained in a band comigrating with albumin. GGE of centrifugally prepared LDL shows the presence of apoB, apoE, and apoD, but not that of apoA-I. However, the particles containing apoA-I, which, in serum, migrated within the LDL size range and as bands of 815 to 345 kDa, were recovered upon centrifugation in the d greater than 1.21 g/ml fraction. GGE of high density lipoproteins (HDL) indicated that most of apoA-I, A

  10. Segmentation of 2D gel electrophoresis spots using a Markov random field

    NASA Astrophysics Data System (ADS)

    Hoeflich, Christopher S.; Corso, Jason J.

    2009-02-01

    We propose a statistical model-based approach for the segmentation of fragments of DNA as a first step in the automation of the primarily manual process of comparing two or more images resulting from the Restriction Landmark Genomic Scanning (RLGS) method. These 2D gel electrophoresis images are the product of the separation of DNA into fragments that appear as spots on X-ray films. The goal is to find instances where a spot appears in one image and not in another since a missing spot can be correlated with a region of DNA that has been affected by a disease such as cancer. The entire comparison process is typically done manually, which is tedious and very error prone. We pose the problem as the labeling of each image pixel as either a spot or non-spot and use a Markov Random Field (MRF) model and simulated annealing for inference. Neighboring spot labels are then connected to form spot regions. The MRF based model was tested on actual 2D gel electrophoresis images.

  11. Fast reversible single-step method for enhanced band contrast of polyacrylamide gels for automated detection.

    PubMed

    Ling, Wei-Li; Lua, Wai-Heng; Gan, Samuel Ken-En

    2015-05-01

    Staining SDS-PAGE is commonly used in protein analysis for many downstream characterization processes. Although staining and destaining protocols can be adjusted, they can be laborious, and faint bands often become false negatives. Similarly, these faint bands hinder automated software band detections that are necessary for quantitative analyses. To overcome these problems, we describe a single-step rapid and reversible method to increase (up to 500%) band contrast in stained gels. Through the use of alcohols, we improved band detection and facilitated gel storage by drying the gels into compact white sheets. This method is suitable for all stained SDS-PAGE gels, including gradient gels and is shown to improve automated band detection by enhanced band contrast. PMID:25782090

  12. Fast reversible single-step method for enhanced band contrast of polyacrylamide gels for automated detection

    PubMed Central

    Ling, Wei-Li; Lua, Wai-Heng; Gan, Samuel Ken-En

    2015-01-01

    Staining SDS-PAGE is commonly used in protein analysis for many downstream characterization processes. Although staining and destaining protocols can be adjusted, they can be laborious, and faint bands often become false negatives. Similarly, these faint bands hinder automated software band detections that are necessary for quantitative analyses. To overcome these problems, we describe a single-step rapid and reversible method to increase (up to 500%) band contrast in stained gels. Through the use of alcohols, we improved band detection and facilitated gel storage by drying the gels into compact white sheets. This method is suitable for all stained SDS-PAGE gels, including gradient gels and is shown to improve automated band detection by enhanced band contrast. PMID:25782090

  13. Comparison of the influence of inorganic salts on the NMR dose sensitivity of polyacrylamide-based gel dosimeter

    NASA Astrophysics Data System (ADS)

    Hayashi, S.-I.; Kawamura, H.; Usui, S.; Tominaga, T.

    2013-06-01

    On the NMR dose sensitivities of polyacrylamide-based gel dosimeters irradiated by X-ray, the additive effect of various inorganic salts (electrolytes) is investigated. Among the various combination of cations (Li+, Na+, K+, Mg2+, Ca2+, Sr2+, Ba2+, Zn2+ and Al3+) and anions (Cl-, NO-3 and SO2-4), MgCl2 is shown to be the most effective sensitizer. In the result, it is suggested that the extent of the increase of the dose sensitivity may correlate to the hydration power of cations rather than anions. Contrary to the dose sensitivity enhancement, the depression of melting point caused by the additives is also pointed out.

  14. Investigation of an outbreak of rotavirus infection in geriatric patients by serotyping and polyacrylamide gel electrophoresis (PAGE).

    PubMed

    Steel, H M; Garnham, S; Beards, G M; Brown, D W

    1992-06-01

    An outbreak of rotavirus diarrhoea amongst patients on two wards in a geriatric unit was investigated using polyacrylamide gel electrophoresis (PAGE) and serotyping. There had been no contact between the patients on different wards but some interchange of staff had occurred so it was important to exclude the possibility that the rotavirus had been spread by staff. Two strains of rotavirus were shown to be present, one on each ward. Differences in the electropherotypes and serotypes were demonstrated, showing conclusively that transfer of virus between the wards had not occurred. Thus, serotyping and PAGE are of value in the investigation of rotavirus outbreaks in the hospital setting where cross-infection between wards is suspected. PMID:1321223

  15. 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. PMID:26796977

  16. Novel application of Ag nanoclusters in fluorescent imaging of human serum proteins after native polyacrylamide gel electrophoresis (PAGE).

    PubMed

    Wang, Yanan; Zhang, Jing; Huang, Lingyun; He, Dacheng; Ma, Lin; Ouyang, Jin; Jiang, Fubin

    2012-01-27

    We have developed a novel application for DNA oligonucleotide-stabilized Ag nanoclusters in fluorescent imaging of human serum proteins after native polyacrylamide gel electrophoresis (PAGE). Oligonucleotide-stabilized Ag nanoclusters were used as fluorescent probes for direct detection of proteins after native PAGE. Some relatively low-abundance proteins, such as α-1-antichymotrypsin (ACT) and α-2-glycoprotein 1, zinc (ZAG) were easily detected by oligonucleotide-stabilized Ag nanocluster-based fluorescent imaging and identified by MS and MS/MS techniques, without the need of expensive antibodies or tedious immunoassay procedures. The pH condition for the oligonucleotide-stabilized Ag nanocluster solution was optimized and the possible mechanism of interaction between proteins and DNA oligonucleotide-stabilized Ag nanoclusters was analyzed. As a novel fluorescent detection method it is simple, fast, nontoxic and sensitive, and it shows great analytical potential in proteome research and in biochemistry. PMID:22249908

  17. A Novel Gaussian Extrapolation Approach for 2-D Gel Electrophoresis Saturated Protein Spots.

    PubMed

    Natale, Massimo; Caiazzo, Alfonso; Ficarra, Elisa

    2016-01-01

    Analysis of images obtained from two-dimensional gel electrophoresis (2-D GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software currently available have proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this chapter, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate proteins quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2-D GE images, comparing reconstructed spots with the corresponding non-saturated image. The results demonstrate that the algorithm enables correct spot quantification. PMID:26611417

  18. [Characterization of Acholeplasma Strains by Horizontal Polyacrylamide Flat Gel Electrophoresis (author's transl)].

    PubMed

    Boden, K; Kirchhoff, H

    1977-01-01

    Proteins extracted with phenol-acetic acid-water (2:1:0.5, w/v/v) from Acholeplasma laidlawii (PG 8), A. granularum (BTS-39), A. oculi (19L), A. modicum (PG 49), A. axanthum (S743) and the Acholeplasma strains C1 and C112 (which were isolated from aborted horse foetuses) were compared by electrophoresis in horizontal acidic polyacylamide flat gel using the electrophoresis equipment LKB Multiphor 2117. In this system the gels are not prepared in the electrophoresis chamber but between glas plates. For electrophoresis they are applied onto a special cooling plate. This makes it possible to produce a number of identical gels (from the same gel mixture and polymerized under the same conditions) what can be important for comparing investigations. The gels can be stored for more than 4 weeks in the refrigerator at +4 degrees C. Marked differences were observed between the electrophoretic patterns of each of the established species and the horse strains C1 and C112. The results are in agreement with those obtained in serological investigations in which the strains C1 and C112 were different from the established Acholeplasma species. PMID:848216

  19. First use of two-dimensional polyacrylamide gel electrophoresis to determine phylogenetic relationships.

    PubMed

    Dopson, Mark; Baker-Austin, Craig; Bond, Philip L

    2004-09-01

    Methods for microbial classification are not always capable of distinguishing between isolates at the species level. We have previously characterised four Ferroplasma isolates that were >98.9% similar at the 16S rDNA level, the isolates showed marked phenotypic differences, and one isolate was borderline on the 70% species boundary from DNA-DNA similarity data. In this study we have used statistical comparisons of two-dimensional polyacylamide gel electrophoresis gels for classification of closely related isolates. From the protein profile similarities an un-rooted tree was constructed that was congruent with a tree derived from DNA-DNA similarities. PMID:15279933

  20. Rifaximin-mediated changes to the epithelial cell proteome: 2-D gel analysis.

    PubMed

    Schrodt, Caroline; McHugh, Erin E; Gawinowicz, Mary Ann; Dupont, Herbert L; Brown, Eric L

    2013-01-01

    Rifaximin is a semi-synthetic rifamycin derivative that is used to treat different conditions including bacterial diarrhea and hepatic encephalopathy. Rifaximin is of particular interest because it is poorly adsorbed in the intestines and has minimal effect on colonic microflora. We previously demonstrated that rifaximin affected epithelial cell physiology by altering infectivity by enteric pathogens and baseline inflammation suggesting that rifaximin conferred cytoprotection against colonization and infection. Effects of rifaximin on epithelial cells were further examined by comparing the protein expression profile of cells pretreated with rifaximin, rifampin (control antibiotic), or media (untreated). Two-dimensional (2-D) gel electrophoresis identified 36 protein spots that were up- or down-regulated by over 1.7-fold in rifaximin treated cells compared to controls. 15 of these spots were down-regulated, including annexin A5, intestinal-type alkaline phosphatase, histone H4, and histone-binding protein RbbP4. 21 spots were up-regulated, including heat shock protein (HSP) 90α and fascin. Many of the identified proteins are associated with cell structure and cytoskeleton, transcription and translation, and cellular metabolism. These data suggested that in addition to its antimicrobial properties, rifaximin may alter host cell physiology that provides cytoprotective effects against bacterial pathogens. PMID:23922656

  1. Rifaximin-Mediated Changes to the Epithelial Cell Proteome: 2-D Gel Analysis

    PubMed Central

    Schrodt, Caroline; McHugh, Erin E.; Gawinowicz, Mary Ann; DuPont, Herbert L.; Brown, Eric L.

    2013-01-01

    Rifaximin is a semi-synthetic rifamycin derivative that is used to treat different conditions including bacterial diarrhea and hepatic encephalopathy. Rifaximin is of particular interest because it is poorly adsorbed in the intestines and has minimal effect on colonic microflora. We previously demonstrated that rifaximin affected epithelial cell physiology by altering infectivity by enteric pathogens and baseline inflammation suggesting that rifaximin conferred cytoprotection against colonization and infection. Effects of rifaximin on epithelial cells were further examined by comparing the protein expression profile of cells pretreated with rifaximin, rifampin (control antibiotic), or media (untreated). Two-dimensional (2-D) gel electrophoresis identified 36 protein spots that were up- or down-regulated by over 1.7-fold in rifaximin treated cells compared to controls. 15 of these spots were down-regulated, including annexin A5, intestinal-type alkaline phosphatase, histone H4, and histone-binding protein RbbP4. 21 spots were up-regulated, including heat shock protein (HSP) 90α and fascin. Many of the identified proteins are associated with cell structure and cytoskeleton, transcription and translation, and cellular metabolism. These data suggested that in addition to its antimicrobial properties, rifaximin may alter host cell physiology that provides cytoprotective effects against bacterial pathogens. PMID:23922656

  2. 2D gel blood serum biomarkers reveal differential clinical proteomics of the neurodegenerative diseases.

    PubMed

    Sheta, Essam A; Appel, Stanley H; Goldknopf, Ira L

    2006-02-01

    This review addresses the challenges of neuroproteomics and recent progress in biomarkers and tests for neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. The review will discuss how the application of quantitative 2D gel electrophoresis, combined with appropriate single-variable and multivariate biostatistics, allows for selection of disease-specific serum biomarkers. It will also address how the use of large cohorts of specifically targeted patient blood serum samples and complimentary age-matched controls, in parallel with the use of selected panels of these biomarkers, are being applied to the development of blood tests to specifically address unmet pressing needs in the differential diagnosis of these diseases, and to provide potential avenues for mechanism-based drug targeting and treatment monitoring. While exploring recent findings in this area, the review discusses differences in critical pathways of immune/inflammation and amyloid formation between Parkinson's disease and amyotrophic lateral sclerosis, as well as discernable synergistic relationships between these pathways that are revealed by this approach. The potential for pathway measurement in blood tests for differential diagnosis, disease burden and therapeutic monitoring is also outlined. PMID:16445350

  3. Differential proteomic profiles from distinct Toxoplasma gondii strains revealed by 2D-difference gel electrophoresis.

    PubMed

    Zhou, Huaiyu; Zhao, Qunli; Das Singla, Lachhman; Min, Juan; He, Shenyi; Cong, Hua; Li, Ying; Su, Chunlei

    2013-04-01

    Toxoplasma gondii is an obligate intracellular protozoan that infects mammals and birds. Human infection during pregnancy may cause severe damage to the fetus. Reactivation of latent infection in immunocompromised patients can cause life-threatening encephalitis. T. gondii strains are highly diverse but only a few lineages (Type I, II and III) are widely spread. In mouse model, Type I strains are highly virulent, whereas Type II and III strains are intermediately or non virulent. It is not clear how much quantitative difference exists in proteomic profiles among these distinct T. gondii lineages. In the present study, the proteomic profiles of T. gondii tachyzoites from these lineages were investigated by two dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrometry (MS) technologies. A total of 2321 protein spots were detected. Overall, the GT1 strain of Type I lineage and the strain PTG of Type II lineage have highly similar proteomic profiles and both are different from that of the CTG strain of Type III lineage. Eighty-four protein spots were differentially expressed by greater than 1.5-fold in relative abundance and 10 of them were identified to 7 T. gondii proteins in existing database. Investigation of the quantitative differences in proteomics among distinct T. gondii strains should facilitate our understanding of difference in biological processes and pathogenesis of distinct T. gondii genotypes, which will provide basic information to determine treatment regimen for different manifestation of toxoplasmosis. PMID:23340323

  4. Chiral discrimination of amines by anisotropic NMR parameters using chiral polyacrylamide-based gels.

    PubMed

    Schmidt, Manuel; Sun, Han; Leonov, Andrei; Griesinger, Christian; Reinscheid, Uwe M

    2012-12-01

    A new chiral alignment medium for dimethyl sulfoxide, methanol, and water as solvents was developed. Because both enantiomers of the gel are available, it is possible to enantiodiscriminate natural products such as strychnine HCl that naturally occurs as single enantiomer. With the two methods of achieving anisotropy, namely stretching and confinement, the degree of alignment can be adjusted, and the director changed from horizontal to vertical. This increases the applicability. Three compounds were enantiodiscriminated on the basis of residual dipolar coupling data: mefloquine HCl, strychnine HCl, and menthylamine HCl. PMID:23280659

  5. Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow

    PubMed Central

    Morisawa, Hiraku; Hirota, Mikako; Toda, Tosifusa

    2006-01-01

    Background In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. Results We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. Conclusion Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved. PMID:17018156

  6. Fast and sensitive colloidal coomassie G-250 staining for proteins in polyacrylamide gels.

    PubMed

    Dyballa, Nadine; Metzger, Sabine

    2009-01-01

    Coomassie Brilliant Blue (CBB) is a dye commonly used for the visualization of proteins separated by SDS-PAGE, offering a simple staining procedure and high quantitation. Furthermore, it is completely compatible with mass spectrometric protein identification. But despite these advantages, CBB is regarded to be less sensitive than silver or fluorescence stainings and therefore rarely used for the detection of proteins in analytical gel-based proteomic approaches. Several improvements of the original Coomassie protocol(1) have been made to increase the sensitivity of CBB. Two major modifications were introduced to enhance the detection of low-abundant proteins by converting the dye molecules into colloidal particles: In 1988, Neuhoff and colleagues applied 20% methanol and higher concentrations of ammonium sulfate into the CBB G-250 based staining solution(2), and in 2004 Candiano et al. established Blue Silver using CBB G-250 with phosphoric acid in the presence of ammonium sulfate and methanol(3). Nevertheless, all these modifications just allow a detection of approximately 10 ng protein. A widely fameless protocol for colloidal Coomassie staining was published by Kang et al. in 2002 where they modified Neuhoff's colloidal CBB staining protocol regarding the complexing substances. Instead of ammonium sulfate they used aluminum sulfate and methanol was replaced by the less toxic ethanol(4). The novel aluminum-based staining in Kang's study showed superior sensitivity that detects as low as 1 ng/band (phosphorylase b) with little sensitivity variation depending on proteins. Here, we demonstrate application of Kang's protocol for fast and sensitive colloidal Coomassie staining of proteins in analytical purposes. We will illustrate the quick and easy protocol using two-dimensional gels routinely performed in our working group. PMID:19684561

  7. 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. PMID:19146099

  8. Polyacrylamide Gel-Entrapped Fungal Manganese Peroxidase from Ganoderma lucidum IBL-05 with Enhanced Catalytic, Stability, and Reusability Characteristics.

    PubMed

    Bilal, Muhammad; Asgher, Muhammad; Iqbal, Hafiz M N

    2016-01-01

    In the present study, polyacrylamide gel (PAG) was utilized as bolster material for the immobilization of in-house extracted and partially purified manganese peroxidase (MnP) through an entrapment technique yielding significant MnP immobilization (87.3±3.3 %) and remarkable stability of the enzyme (37.2±2.4 %) after a storage period of two months at 4°C. The immobilization also increased the optimal temperature by 10 °C and provided an alkaline shift of the pH optimum. Moreover, a significant enhancement in the thermo-stability was observed. After an incubation period of 72 h at 50°C, the PAG-entrapped-MnP still exhibited 41.2 % of the initial activity, whereas the free enzyme was completely inactive. Furthermore, PAG-entrapped-MnP showed an excellent recycling efficiency and retained more than 50% of its initial activity after five consecutive reaction cycles. In conclusion, owing to the economic feasibility, carrier-supported MnP may be a promising candidate for various applications in different industrial sectors. PMID:27531237

  9. Genetic diversity analysis of faba bean (Vicia faba L.) germplasms using sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

    PubMed

    Hou, W W; Zhang, X J; Shi, J B; Liu, Y J

    2015-01-01

    To investigate genetic diversity and relationships of 101 faba bean (Vicia faba L.), landraces and varieties from different provinces of China and abroad were analyzed by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE). A total of 2625 unambiguous and stable bands from 101 germplasms were detected, and 36 different bands were classified according to the electrophoretic mobility patterns of the proteins as determined by the SDS-PAGE analysis, of which 16 were polymorphic. Besides the common bands, the protein bands of 92, 75, 62, 40, 34, 17, and 13 kDa presented the highest frequencies of 92.08, 90.10, 99.01, 95.05, 95.05, 98.02, and 95.05%, respectively. The other 29 polymorphic protein bands showed higher polymorphism with 16.09 polymorphic bands in average. The genetic similarity of the 101 genotypes tested varied from 0.6111 to 0.9722, with an average of 0.7122. Cluster analysis divided the 101 genotypes into six major clusters, which was consistent with the systematic classification of faba bean done in previous studies. The overall results indicated that SDS-PAGE was a useful tool for genetic diversity analysis and laid a solid foundation for future faba bean breeding. PMID:26535710

  10. Assessing the stability of cystatin/cysteine proteinase complexes using mildly-denaturing gelatin-polyacrylamide gel electrophoresis.

    PubMed

    Michaud, D; Cantin, L; Raworth, D A; Vrain, T C

    1996-01-01

    A method for assessing the stability of cystatin/cysteine proteinase complexes using mildly-denaturing gelatin-polyacrylamide gel electrophoresis (gelatin-PAGE) is described. As suggested by the use of well-known cystatins (human stefins A and B, and oryzacystatins I and II) and the plant cysteine proteinase papain, the ability of cystatin/cysteine proteinase complexes to remain stable during electrophoresis is associated with the degree of affinity between the enzyme and the inhibitor (and inversely associated with the Ki values), at least with the disulfide bond-lacking cystatins. Complexes with Ki values > or = 10(-8) M (weak interactions) are partly or completely dissociated under the conditions used, while those with lower Ki values (strong interactions) remain stable. As shown by the differential effects of two plant cystatins, oryzacystatins I and II, against a cysteine proteinase present in crude (complex) extracts from a plant pest -- the two-spotted spider mite (Tetranychus urticae Koch), the gelatin-PAGE procedure is suitable for studying the ability of cystatins to form highly stable complexes with cysteine proteinases, without the need for prior purification steps. Considering the well-recognized potential of proteinase inhibitors for pest and pathogen control, this analytical approach will be useful for rapidly assessing the respective potential of various cystatins for protection of plants, animals, and humans. PMID:8907521

  11. Serum sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of patients with membranous nephropathy and focal and segmental glomerulosclerosis.

    PubMed

    Pant, Pragya; Singh, R G; Singh, Santosh K; Singh, Vijay P; Doley, Prodip K; Sivasankar, M

    2016-01-01

    Diagnosis of membranous nephropathy (MN) and focal and segmental glomerulo- sclerosis (FSGS) needs a renal biopsy, which is an invasive procedure with potentially serious complications. Proteomics may be applied for the development of a biomarker for these diseases which will obviate the need of biopsy. Serum sodium dodecyl sulfate-polyacrylamide gel electro-phoresis (SDS-PAGE) analysis gives an idea of the various proteins with different molecular weights (MWs) in a given sample. This study was conducted to analyze proteins with different MWs in patients with MN and FSGS and to compare the two groups with regard to their protein profile. This was a comparative, experimental study performed from June 2013 to July 2014 in the Department of Nephrology, Sir Sunderlal Hospital, Banaras Hindu University, Varanasi. Twenty-three histologically diagnosed cases of primary MN and 25 cases of FSGS were included in the study. Patients were categorized as having mild, moderate, and severe proteinuria with 24 h urinary protein levels of <4, 4- 8 and ≥8 g/24 h, respectively. SDS-PAGE analysis was performed by the method of Laemmli and revealed a significantly higher number of patients with FSGS (80%) having a protein corresponding to 29 kDa MW, than those with MN (39.1%) (P = 0.004). Protein of 5 kDa MW was present in a significantly higher number of patients with moderate (80%) and severe (100%) proteinuria than those with mild proteinuria (25%) (P <0.001). Thus, protein of MW 29 kDa may be a marker for FSGS and needs further characterization. Similarly, 5 kDa protein, present in patients with moderate and severe proteinuria, might be either contributing to or be a marker of severe illness. PMID:27215247

  12. Identification of stable plant cystatin/nematode proteinase complexes using mildly denaturing gelatin/polyacrylamide gel electrophoresis.

    PubMed

    Michaud, D; Cantin, L; Bonadé-Bottino, M; Jouanin, L; Vrain, T C

    1996-08-01

    The biochemical interactions between two cystatins from rice seeds, oryzacystatin I (OCI) and oryzacystatin II (OCII), and the cysteine proteinases from three plant parasitic nematodes, Meloidogyne hapla, M. incognita and M. javanica, were assessed using standard protease assays and mildly denaturing gelatin/polyacrylamide gel electrophoresis (gelatin/PAGE). Activity detected in extracts of preparasitic second-stage larvae (J2) from M. hapla was optimal at pH 5.5 and was inhibited in vitro by the cysteine proteinase inhibitors trans-epoxysuccinyl-L-leucylamido-(4-guanidino) butane, hen egg cystatin, OCI, and OCII. As demonstrated by class-specific activity staining, all the activity measured between pH 3.5 and pH 7.5 was accounted for by a major proteinase form, Mhp1, and two minor forms, Mhp2 and Mhp3. Mhps were also detected in extracts and excretions of parasitic J2 and adult females, indicating their continuous expression throughout development of M. hapla, and their possible involvement in the extracellular degradation of proteins. Interestingly, the two plant cysteine proteinase inhibitors OCI and OCII showed different degrees of affinity for the major proteinase form, Mhp1. Both inhibitors almost completely inactivated this proteinase in native conditions but, unlike OCII, OCI conserved a high affinity for Mhp1 during mildly denaturing gelatin/PAGE, showing the differential stabilities of the OCI/Mhp1 and OCII/Mhp1 complexes. In contrast to Mhp1, the major cysteine proteinases detected in the two closely related species M. incognita and M. javanica were strongly inhibited by OCII, while the inhibition of OCI was partly prevented during electrophoresis. This species-related efficiency of plant cystatins against nematode cysteine proteinases could have practical implications when planning their use to control nematodes of the genus Meloidogyne. PMID:8874065

  13. Comparative two-dimensional polyacrylamide gel electrophoresis of the salivary proteome of children with autism spectrum disorder

    PubMed Central

    Ngounou Wetie, Armand G; Wormwood, Kelly L; Charette, Laci; Ryan, Jeanne P; Woods, Alisa G; Darie, Costel C

    2015-01-01

    In the last decades, prevalence of autism spectrum disorder (ASD) has been on the rise. However, clear aetiology is still elusive and improvements in early diagnosis are needed. To uncover possible biomarkers present in ASD, we used two-dimensional polyacrylamide gel electrophoresis and nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS), to compare salivary proteome profiling of children with ASD and controls. A total of 889 spots were compared and only those spots with a fold change ≥1.7 and a P-value <0.05 or a fold change of ≥3.0 between ASD cases and controls were analysed by nanoLC-MS/MS. Alpha-amylase, CREB-binding protein, p532, Transferrin, Zn alpha2 glycoprotein, Zymogen granule protein 16, cystatin D and plasminogen were down-regulated in ASD. Increased expression of proto-oncogene Frequently rearranged in advanced T-cell lymphomas 1 (FRAT1), Kinesin family member 14, Integrin alpha6 subunit, growth hormone regulated TBC protein 1, parotid secretory protein, Prolactin-inducible protein precursor, Mucin-16, Ca binding protein migration inhibitory factor-related protein 14 (MRP14) was observed in individuals with ASD. Many of the identified proteins have previously been linked to ASD or were proposed as risk factors of ASD at the genetic level. Some others are involved in pathological pathways implicated in ASD causality such as oxidative stress, lipid and cholesterol metabolism, immune system disturbances and inflammation. These data could contribute to protein signatures for ASD presence, risk and subtypes, and advance understanding of ASD cause as well as provide novel treatment targets for ASD. PMID:26290361

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

    SciTech Connect

    Ono, K; Fujimoto, S; Akagi, Y; Hirokawa, Y; Hayashi, S; Miyazawa, M

    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 T 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.

  15. A highly sensitive "turn-on" fluorescent sensor for the detection of human serum proteins based on the size exclusion of the polyacrylamide gel.

    PubMed

    Xu, Shenghao; Liu, Pingping; Lu, Xin; Zhang, Jing; Huang, Lingyun; Hua, Wenhao; He, Dacheng; Ouyang, Jin

    2014-02-01

    A highly sensitive "turn-on" fluorescent sensor based on the size exclusion of the polyacrylamide gel was developed for the on-gels detection of human serum proteins after PAGE. The possible mechanism of this fluorescence sensor was illustrated and validated by utilizing five kinds of colloidal silver nanoparticles with different particle size distribution and six kinds of polyacrylamide gels with different pore size. It was attributed to that silver nanoparticles (<5 nm in diameter) had been selectively absorbed into the gel and formed the small silver nanoclusters, resulting in the red fluorescence. Using this new technique for the detection of human serum proteins after PAGE, a satisfactory sensitivity was achieved and some relatively low-abundance proteins (e.g. zinc-alpha-2-glycoprotein), which are the significant proteinic markers of certain diseases can be easily detected, but not with traditional methods. Furthermore, it was also successfully applied to distinguish between serums from hepatoma patient and healthy people. As a new protein detection technique, the colloidal silver nanoparticles based "turn-on" fluorescent sensor offers a rapid, economic, low background, and sensitive way for direct detection of human serum proteins, showing available potential and significance in the development of nanobiotechnology and proteome research. PMID:24150987

  16. An electroblotting, two-step procedure for the detection of proteinases and the study of proteinase/inhibitor complexes in gelatin-containing polyacrylamide gels.

    PubMed

    Visal-Shah, S; Vrain, T C; Yelle, T C; Nguyen-Quoc, B; Michaud, D

    2001-08-01

    A two-step gelatin/polyacrylamide gel electrophoresis (gelatin/PAGE) procedure was devised for the detection of proteinases and the study of proteinase/inhibitor interactions in complex biological extracts. The proteins are first resolved by sodium dodecyl sulfate (SDS)-PAGE under reducing or nonreducing conditions, and electrotransferred into a 0.75 mm-thick accompanying polyacrylamide slab gel containing 0.1% w/v porcine gelatin. The active proteinase bands are developed by a gelatin proteolysis step in the accompanying gel in the presence or absence of diagnostic proteinase inhibitors, allowing the assessment of proteinase classes and the visual discrimination of inhibitor-'sensitive' and -'insensitive' proteinases in complex extracts. Alternatively, protein extracts are preincubated with specific reversible inhibitors before electrophoresis, allowing a rapid discrimination of strong and weak interactions implicating proteinases and reversible inhibitors. In comparison with the standard gelatin/PAGE procedure, that involves copolymerization of gelatin with acrylamide in the resolving gel, this new procedure simplifies proteinase patterns, avoids overestimation of proteinase numbers in complex extracts, and allows in certain conditions the estimation of proteinase molecular weights. Stem bromelain (EC 3.4.22.32), bovine trypsin (EC 3.4.21.4), papain (EC 3.4.22.2), and the extracellular (digestive) cysteine proteinases of five herbivorous pests are used as model enzymes to illustrate the usefulness of this approach in detecting proteinases and in studying their interactions with specific proteinaceous inhibitors potentially useful in biotechnology. PMID:11545387

  17. [Modified Gedelisa test (electrophoresis in gradient of polyacrylamide gel combined with Elisa test). Applications to Toxoplasma gondii exo-antigens (author's transl)].

    PubMed

    Desgeorges, P T; Ambroise-Thomas, P; Falanga, P; Renversez, J C

    1980-01-01

    The authors describe a modified Gedelisa test made up an electrophorese in gradient polyacrylamide gel plus an Elisa test. The gel gradient, after electrophoretic migration is cut longitudinaly. One half is stained with Coomassie blue and the second half is cut in slices of 1 mm thick. Each slice is placed in a well of a microtitration polystirene plate, filled up with carbonate buffer pH 9,6 and then scrached. Proteins diffuse out of the gel and coated on the polystirene. The antigenicity of the coated proteins is revealed by Elisa test. This technique was applied to the study of Toxoplasma gondii exo-antigens obtained from medium of in vitro culture on Vero cells. This antigen contains four fractions, three of them are stained with Coomassie blue, their molecular weights are 160 000, 830 000 and more than one million daltons. PMID:7212392

  18. Three-dimensional polyacrylamide gel-based DNA microarray method effectively identifies UDP-glucuronosyltransferase 1A1 gene polymorphisms for the correct diagnosis of Gilbert's syndrome.

    PubMed

    Song, Jinyun; Sun, Mei; Li, Jiayan; Zhou, Dongrui; Wu, Xuping

    2016-03-01

    Gilbert's syndrome is a mild genetic liver disorder characterized by unconjugated hyperbilirubinemia due to defects in the UDP-glucuronosyltransferase 1A1 (UGT1A1) gene. The T-3279G mutation in the phenobarbital responsive enhancer module (PBREM), the TA-insertion in the TATA box, creating the A(TA)7TAA motif instead of A(TA)6TAA and the G211A mutation in coding exon 1, particularly in Asian populations, of the human UGT1A1 gene are the three common genotypes found in patients with Gilbert's syndrome. Different approaches for detecting the T-3279G, A(TA)6/7TAA and G211A mutations of the UGT1A1 gene have been described. In this study, to the best of our knowledge, we established a three-dimensional polyacrylamide gel-based DNA microarray method for the first time, in order to study UGT1A1 gene polymorphisms. This method, based on a step-by-step three-dimensional polyacrylamide gel-based DNA microarray protocol, successfully identified all possible genotypes of T-3279G, A(TA)6/7TAA and G211A in 20 patients with hyperbilirubinemia. In addition, sequencing was performed to confirm these results. The data from the current study demonstrate that the three-dimensional polyacrylamide gel microarray method has the potential to be applied as a useful, reliable and cost-effective tool to detect the T-3279G, the A(TA)6/7TAA and the G211A mutations of the UGT1A1 gene in patients with hyperbilirubinemia and thereby aid in the diagnosis of Gilbert's syndrome. PMID:26781906

  19. Three-dimensional polyacrylamide gel-based DNA microarray method effectively identifies UDP-glucuronosyltransferase 1A1 gene polymorphisms for the correct diagnosis of Gilbert's syndrome

    PubMed Central

    SONG, JINYUN; SUN, MEI; LI, JIAYAN; ZHOU, DONGRUI; WU, XUPING

    2016-01-01

    Gilbert's syndrome is a mild genetic liver disorder characterized by unconjugated hyperbilirubinemia due to defects in the UDP-glucuronosyltransferase 1A1 (UGT1A1) gene. The T-3279G mutation in the phenobarbital responsive enhancer module (PBREM), the TA-insertion in the TATA box, creating the A(TA)7TAA motif instead of A(TA)6TAA and the G211A mutation in coding exon 1, particularly in Asian populations, of the human UGT1A1 gene are the three common genotypes found in patients with Gilbert's syndrome. Different approaches for detecting the T-3279G, A(TA)6/7TAA and G211A mutations of the UGT1A1 gene have been described. In this study, to the best of our knowledge, we established a three-dimensional polyacrylamide gel-based DNA microarray method for the first time, in order to study UGT1A1 gene polymorphisms. This method, based on a step-by-step three-dimensional polyacrylamide gel-based DNA microarray protocol, successfully identified all possible genotypes of T-3279G, A(TA)6/7TAA and G211A in 20 patients with hyperbilirubinemia. In addition, sequencing was performed to confirm these results. The data from the current study demonstrate that the three-dimensional polyacrylamide gel microarray method has the potential to be applied as a useful, reliable and cost-effective tool to detect the T-3279G, the A(TA)6/7TAA and the G211A mutations of the UGT1A1 gene in patients with hyperbilirubinemia and thereby aid in the diagnosis of Gilbert's syndrome. PMID:26781906

  20. Fluid diversion and sweep improvement with chemical gels in oil recovery processes. [Four types of gels: resorcinol-formaldehyde; colloidal silica; Cr sup 3+ (chloride)-xanthan; and Cr sup 3+ (acetate)-polyacrylamide

    SciTech Connect

    Seright, R.S.; Martin, F.D.

    1992-09-01

    The objectives of this project were to identify the mechanisms by which gel treatments divert fluids in reservoirs and to establish where and how gel treatments are best applied. Several different types of gelants were examined, including polymer-based gelants, a monomer-based gelant, and a colloidal-silica gelant. This research was directed at gel applications in water injection wells, in production wells, and in high-pressure gas floods. The work examined how the flow properties of gels and gelling agents are influenced by permeability, lithology, and wettability. Other goals included determining the proper placement of gelants, the stability of in-place gels, and the types of gels required for the various oil recovery processes and for different scales of reservoir heterogeneity. During this three-year project, a number of theoretical analyses were performed to determine where gel treatments are expected to work best and where they are not expected to be effective. The most important, predictions from these analyses are presented. Undoubtedly, some of these predictions will be controversial. However, they do provide a starting point in establishing guidelines for the selection of field candidates for gel treatments. A logical next step is to seek field data that either confirm or contradict these predictions. The experimental work focused on four types of gels: (1) resorcinol-formaldehyde, (2) colloidal silica, (3) Cr{sup 3+}(chloride)-xanthan, and (4) Cr{sup 3+}(acetate)-polyacrylamide. All experiments were performed at 41{degrees}C.

  1. Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani.

    PubMed

    Schmidt-Arras, Dirk; Leclercq, Olivier; Gherardini, Pier Federico; Helmer-Citterich, Manuela; Faigle, Wolfgang; Loew, Damarys; Späth, Gerald F

    2011-08-24

    The protozoan parasite Leishmania donovani undergoes various developmental transitions during its infectious cycle that are triggered by environmental signals encountered inside insect and vertebrate hosts. Intracellular differentiation of the pathogenic amastigote stage is induced by pH and temperature shifts that affect protein kinase activities and downstream protein phosphorylation. Identification of parasite proteins with phosphotransferase activity during intracellular infection may reveal new targets for pharmacological intervention. Here we describe an improved protocol to trace this activity in L. donovani extracts at high resolution combining in-gel kinase assay and two-dimensional gel electrophoresis. This 2D procedure allowed us to identify proteins that are associated with amastigote ATP-binding, ATPase, and phosphotransferase activities. The 2D in-gel kinase assay, in combination with recombinant phospho-protein substrates previously identified by phospho-proteomics analyses, provides a novel tool to establish specific protein kinase-substrate relationships thus improving our understanding of Leishmania signal transduction with relevance for future drug development. PMID:21443974

  2. Introducing Proteomics in the Undergraduate Curriculum: A Simple 2D Gel Electrophoresis Exercise with Serum Proteins

    ERIC Educational Resources Information Center

    Kim, Thomas D.; Craig, Paul A.

    2010-01-01

    Two-dimensional gel electrophoresis (2DGE) remains an important tool in the study of biological systems by proteomics. While the use of 2DGE is commonplace in research publications, there are few instructional laboratories that address the use of 2DGE for analyzing complex protein samples. One reason for this lack is the fact that the preparation…

  3. Identification of Methanococcus Jannaschii Proteins in 2-D Gel Electrophoresis Patterns by Mass Spectrometry

    DOE R&D Accomplishments Database

    Liang, X.

    1998-06-10

    The genome of Methanococcus jannaschii has been sequenced completely and has been found to contain approximately 1,770 predicted protein-coding regions. When these coding regions are expressed and how their expression is regulated, however, remain open questions. In this work, mass spectrometry was combined with two-dimensional gel electrophoresis to identify which proteins the genes produce under different growth conditions, and thus investigate the regulation of genes responsible for functions characteristic of this thermophilic representative of the methanogenic Archaea.

  4. Identification of methanococcus jannaschii proteins in 2-D gel electrophoresis patterns by mass spectrometry.

    SciTech Connect

    Liang, X.

    1998-06-10

    The genome of Methanococcus jannaschii has been sequenced completely and has been found to contain approximately 1,770 predicted protein-coding regions. When these coding regions are expressed and how their expression is regulated, however, remain open questions. In this work, mass spectrometry was combined with two-dimensional gel electrophoresis to identify which proteins the genes produce under different growth conditions, and thus investigate the regulation of genes responsible for functions characteristic of this thermophilic representative of the methanogenic Archaea.

  5. 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

    2006-01-01

    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. PMID:16378447

  6. Coloration of silver-stained protein bands in polyacrylamide gels is caused by light scattering from silver grains of characteristic sizes.

    PubMed Central

    Merril, C R; Bisher, M E; Harrington, M; Steven, A C

    1988-01-01

    This study investigates the physical basis of color effects in the detection of proteins in polyacrylamide gels by silver staining. Specifically, the hypothesis that different colors may correlate with the development of silver grains of characteristic sizes was investigated by electron microscopy. Protein bands that stained brown, yellow, and blue were excised from stained gels and prepared for electron microscopy by thin-sectioning. In each case, the size distributions of globular silver grains were determined directly from the electron micrographs. We found that blue bands have larger silver grains (with diameters of 40-100 nm) than yellow (21-39 nm) or brown bands (17-35 nm). On the basis of these and other observations, a general mechanism is proposed whereby chemical specificity of electrophoretically separated proteins is expressed in color-specific silver staining. Images PMID:2448776

  7. Analysis of HeLa cell hypoxanthine phosphoribosyltransferase mutants and revertants by two-dimensional polyacrylamide gel electrophoresis: evidence for silent gene activation.

    PubMed Central

    Milman, G; Lee, E; Ghangas, G S; McLaughlin, J R; George, M

    1976-01-01

    The spot corresponding to hypoxanthine phosphoribosyltransferase (HPRT; IMP:pyrophosphate phosphoribosyltransferase, EC 2.4.2.8) has been identified in two-dimensional polyacrylamide gels of HeLa cell extracts. This spot is absent in gels of 24 HPRT dificient mutants. A missense mutant displays a new HPRT spot at the same molecular weight but different isoelectric focusing position. Five independently isolated revertants of the missense mutant display spots corresponding to both the wild-type and mutant proteins indicating that they synthesize HPRT from two separate genes. If the missense protein is synthesized from a mutated form of the initially active HPRT gene, then wild-type HPRT protein in the revertants must be snythesized from a newly activated but prevously silent wild-type gene. The newly activated gene in the revertants of the missense mutation appears unstable producing a high frequency of spontaneous HPRT mutants. Images PMID:63948

  8. Fuzzy watershed segmentation algorithm: an enhanced algorithm for 2D gel electrophoresis image segmentation.

    PubMed

    Rashwan, Shaheera; Sarhan, Amany; Faheem, Muhamed Talaat; Youssef, Bayumy A

    2015-01-01

    Detection and quantification of protein spots is an important issue in the analysis of two-dimensional electrophoresis images. However, there is a main challenge in the segmentation of 2DGE images which is to separate overlapping protein spots correctly and to find the weak protein spots. In this paper, we describe a new robust technique to segment and model the different spots present in the gels. The watershed segmentation algorithm is modified to handle the problem of over-segmentation by initially partitioning the image to mosaic regions using the composition of fuzzy relations. The experimental results showed the effectiveness of the proposed algorithm to overcome the over segmentation problem associated with the available algorithm. We also use a wavelet denoising function to enhance the quality of the segmented image. The results of using a denoising function before the proposed fuzzy watershed segmentation algorithm is promising as they are better than those without denoising. PMID:26510287

  9. GEL-STATE NMR OF BALL-MILLED WHOLE CELL WALLS IN DMSO-d6 USING 2D SOLUTION-STATE NMR SPECTROSCOPY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant cell walls were used for obtaining 2D solution-state NMR spectra without actual solubilization or structural modification. Ball-milled whole cell walls were swelled directly in the NMR tube with DMSO-d6 where they formed a gel. There are relatively few gel-state NMR studies. Most have involved...

  10. 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. PMID:23958139

  11. A computational study into the use of polyacrylamide gel and A-150 plastic as brain tissue substitutes for boron neutron capture therapy

    NASA Astrophysics Data System (ADS)

    Wojnecki, C.; Green, S.

    2001-05-01

    A precise evaluation of the dosimetric performance of epithermal neutron beams designed for boron neutron capture theory of brain tumours requires the use of a phantom material that closely matches brain tissue. The aim of this study was to investigate how well polyacrylamide gel (or PAG) and A-150 plastic performed as substitutes for brain tissue compared with standard phantom materials such as water and polymethyl-methacrylate (or PMMA). Thermal neutron fluence, photon dose and epithermal neutron dose distributions were calculated for the epithermal neutron beam available at the University of Birmingham. The results presented in this paper show that the PAG provides a good simulation of radiation transport in the brain with differences from the real brain of + 9.4%, -10.8% and + 5.1% at a depth of 50 mm for thermal neutron fluence, gamma dose and epithermal neutron dose distributions respectively. The polyacrylamide gel presented is therefore a promising substitute for brain tissue that can, as a dosimeter, provide a three-dimensional map of the absorbed dose delivered by the epithermal neutron beam. However, this study does not investigate the agreement between doses derived from magnetic resonance and physical doses for such gels. A-150 plastic was shown to be a better substitute for brain tissue than PMMA, with differences from brain of -1.9%, -12.4% and -13.2% at a depth of 50 mm for thermal neutron fluence, gamma dose and epithermal neutron dose distributions respectively, against + 21.1%, -16.2% and + 19.2% for PMMA. A-150 plastic should therefore be the material of choice for solid phantoms.

  12. Analysis of the sodium dodecyl sulfate-stable peptidoglycan autolysins of select gram-negative pathogens by using renaturing polyacrylamide gel electrophoresis.

    PubMed Central

    Bernadsky, G; Beveridge, T J; Clarke, A J

    1994-01-01

    For the first time, peptidoglycan autolysins from cellular fractions derived from sonicated cultures of Pseudomonas aeruginosa PAO1, Escherichia coli W7, Klebsiella pneumoniae CWK2, and Proteus mirabilis 19 were detected and partially characterized by zymogram analysis. Purified murein sacculi from P. aeruginosa PAO1 were incorporated into a sodium dodecyl sulfate (SDS)-polyacrylamide gel at a concentration of 0.05% (wt/vol) to serve as a substrate for the separated autolysins. At least 11 autolysin bands of various intensities with M(r)s ranging between 17,000 and 122,000 were detected in each of the homogenated cultures. Some of the autolysins of the four bacteria had similar M(r)s. The zymogram analysis was used to show that a number of the autolysins from E. coli were inhibited by the heavy metals Hg2+ and Cu2+, at 1 and 10 mM, respectively, high ionic strengths, and reagents known to affect the packing of lipopolysaccharides. The activity of an autolysin with an M(r) of 65,000 was also impaired by penicillin G, whereas it was enhanced by gentamicin. A preliminary screen to determine the relationship between penicillin-binding proteins (PBPs) and autolysins was carried out by using a dual assay in which radiolabelled penicillin V bands were visualized on an autolysin zymogram. Radiolabelled bands corresponding to PBPs 3, 4, 5, and 6 from E. coli and P. aeruginosa; PBPs 3, 4, and 6 from Proteus mirabilis; and PBP 6 from K. pneumoniae degraded the murein sacculi in the gels and were presumed to have autolytic activity, although the possibility of two distinct enzymes, each with one of the activities, comigrating in the SDS-polyacrylamide gels could not be excluded. Some radiolabelled bands possessed an Mr of <34,000 and coincided with similar low-Mr autolysin bands. Images PMID:7915268

  13. Fluorographic detection of tritiated glycopeptides and oligosaccharides separated on polyacrylamide gels: analysis of glycans from Dictyostelium discoideum glycoproteins

    SciTech Connect

    Prem Das, O.; Henderson, E.J.

    1986-11-01

    Previous workers have shown that oligosaccharides and glycopeptides can be separated by electrophoresis in buffers containing borate ions. However, normal fluorography of tritium-labeled structures cannot be performed because the glycans are soluble and can diffuse during equilibration with scintillants. This problem has been circumvented by equilibration of the gel with 2,5-diphenyloxazole (PPO) prior to electrophoresis. The presence of PPO in the gel during electrophoresis does not alter mobility of the glycopeptides and oligosaccharides. After electrophoresis, the gel is simply dried and fluorography performed. This allows sensitive and precise comparisons of labeled samples in parallel lanes of a slab gel and, since mobilities are highly reproducible, between different gels. The procedure is preparative in that after fluorography the gel bands can be quantitatively eluted for further study, without any apparent modification by the procedure. In this report, the procedure is illustrated by fractionation of both neutral and anionic glycopeptides produced by the cellular slime mold Dictyostelium discoideum.

  14. Novel application of PhastSystem polyacrylamide gel electrophoresis using restriction fragment length polymorphism--internal transcribed spacer patterns of individuals for molecular identification of entomopathogenic nematodes.

    PubMed

    Pamjav, H; Triga, D; Buzás, Z; Vellai, T; Lucskai, A; Adams, B; Reid, A P; Burnell, A; Griffin, C; Glazer, I; Klein, M G; Fodor, A

    1999-06-01

    différences! [editorial] [editorial]onomic way of identifying and assigning nematodes to taxons, which had already been determined either by comparative sequence analysis of nuclear rDNA internal transcribed spacer (ITS) region or by other methods of molecular or conventional taxonomy, is provided. Molecular identification of entomopathogenic nematodes (EPN) can be upgraded by basing it on PhastSystem polyacrylamide gel electrophoresis (PAGE) analysis of restriction fragment length polymorphism (RFLP) patterns of polymerase chain reaction (PCR)-amplified DNA derived from single nematodes of Steinernema or Heterorhabditis spp. Although analysis from single worms has previously been made on agarose gel, the resolution on PhastSystem PAGE gel is much higher. The DNA sequences selected for analysis were those constituting the internal transcribed spacer region between the 18S and 26S rDNA genes within the rRNA operon. RFLP analysis was carried out by gel electrophoresis on the PhastSystem (Pharmacia) as detailed elsewhere (Triga et al., Electrophoresis 1999, 20, 1272-1277. The downscaling from conventional agarose to PhastSystem gels resulted in pattern of DNA fragments differing from those obtained with agarose gel electrophoresis under conventional conditions by increasing the number of detected fragments. The approach supported previous species identifications and was able to identify several unclassified isolates, such as those from Hungary and Ireland, and provides a method for identification of previously unclassified strains. We confirmed that Heterorhabditis "Irish Type", represented by two strains of different geographical origin, comprise a species different from H. megidis. We also confirmed that strain IS5 belongs to the species H. indicus rather than to H. bacteriophora, as had been suggested previously. PMID:10380767

  15. Highly sensitive and simple fluorescence staining of proteins in sodium dodecyl sulfate-polyacrylamide-based gels by using hydrophobic tail-mediated enhancement of fluorescein luminescence.

    PubMed

    Kang, Chulhun; Kim, Hyun Jung; Kang, Donghoon; Jung, Duk Young; Suh, Myungkoo

    2003-10-01

    Fluorescein has an extremely low luminescence intensity in acidic aqueous media. However, when it was bound to proteins, subsequent increase of luminescence intensity took place. Furthermore, when a hydrophobic tail, such as aliphatic hydrocarbons, was introduced to fluorescein, more dramatic increase of luminescence intensity was observed upon binding to proteins. In the present study, by utilizing this luminescence enhancement, three hydrophobic fluorescein dyes (5-dodecanoyl amino fluorescein, 5-hexadecanoyl amino fluorescein, and 5-octadecanoyl amino fluorescein) were examined as noncovalent fluorescent stains of protein bands in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Effective incorporation of the dyes to proteins in gels was accomplished either simply by adding dyes at the protein fixation step, or by treating gels with a staining solution after the fixation. The sensitivity of this staining method using the fluorescein derivatives was approximately 1 ng/band for most proteins. For some cases, protein bands containing as low as 0.1 ng were successfully visualized. In addition, the detection sensitivity showed much less protein-to-protein variation than silver staining. This new staining method was also successfully applied to two-dimensional electrophoresis of rat brain proteins. Its overall sensitivity was comparable to that of silver staining. PMID:14595675

  16. Use of fluorescein hydrazide and fluorescein thiosemicarbazide reagents for the fluorometric determination of protein carbonyl groups and for the detection of oxidized protein on polyacrylamide gels.

    PubMed

    Ahn, B; Rhee, S G; Stadtman, E R

    1987-03-01

    Highly fluorescent thiosemicarbazide and hydrazide prepared by reaction of fluorescein isothiocyanate with hydrazine or adipic acid dihydrazide have been used to monitor the presence of carbonyl groups in oxidatively modified proteins. After oxidation, proteins react with these reagents under anaerobic conditions in the dark to yield fluorescent protein conjugates (presumably thiosemicarbazones or hydrazones) which can be visualized as fluorescent bands following electrophoresis (0-4 degrees C) on lithium dodecyl sulfate-polyacrylamide gels. These reagents do not react with unoxidized proteins. The conjugates formed dissociate readily at room temperature but are fairly stable at pH 6-9, 0 degrees C. Current data suggest that these reagents will be useful in the detection and quantitation of oxidatively modified proteins in biological systems. PMID:2883911

  17. Ten-Year Safety with Polyacrylamide Gel Used to Correct Facial Lipoatrophy in HIV-Infected Patients.

    PubMed

    Negredo, Eugenia; Puig, Jordi; Ornelas, Arelly; Echeverría, Patricia; Bonjoch, Anna; Estany, Carla; Higueras, Carmen; Gonzalez-Mestre, Vicente; Clotet, Bonaventura

    2015-08-01

    Long-term results (>5 years) for synthetic substances used to repair facial lipoatrophy have not been published. We performed a cross-sectional study to evaluate the 10-year safety of polyacrylamide hydrogel (Aquamid) among the 751 patients from our unit who received facial infiltrations at least 10 years ago. Epidemiological and clinical data such as complications and patient satisfaction were collected. We also identified those patients who presented a facial infection at any time after infiltration. A total of 104 patients had received Aquamid at least 10 years ago. Before infiltrations, 24.0%, 41.3%, and 34.7% presented very severe, severe, and moderate facial lipoatrophy, respectively. After a mean (SD) of 10.3 (0.5) years since the infiltrations, 19.2%, 47.7%, and 31.7% of patients reported moderate, mild, and no signs of facial lipoatrophy. The values reported by physicians for the same categories were 1.9%, 10.6%, and 87.5%. Indurations were detected in 6.7% of patients and nodules in 3.8%. Five patients (4.8%) had a local infection. A further 15 patients with a shorter follow-up (less than 10 years) presented local infections (overall incidence considering the 751 patients who received infiltrations of Aquamid, 2.7%); the product had to be withdrawn in three cases. The majority of patients were highly satisfied (74.8%) or satisfied (23.4%) with the cosmetic results; among patients with severe or very severe lipoatrophy at baseline, 31.4% were satisfied and 65.7% were highly satisfied. Infiltrations with polyacrylamide hydrogel (Aquamid) are a safe strategy for the treatment of facial lipoatrophy in the long term. The rate of severe complications was low, and patient satisfaction with the cosmetic results was high. However, facial infections may appear in the long term. Therefore, HIV-infected patients who received synthetic substances should be carefully monitored over time. PMID:25858612

  18. Polyacrylamide gel substrates that simulate the mechanical stiffness of normal and malignant neuronal tissues increase protoporphyin IX synthesis in glioma cells

    NASA Astrophysics Data System (ADS)

    Niu, Carolyn J.; Fisher, Carl; Scheffler, Kira; Wan, Rachel; Maleki, Hoda; Liu, Haijiao; Sun, Yu; Simmons, Craig A.; Birngruber, Reginald; Lilge, Lothar

    2015-09-01

    Protoporphyrin IX (PPIX) produced following the administration of exogenous 5d-aminolevulinic acid is clinically approved for photodynamic therapy and fluorescence-guided resection in various jurisdictions around the world. For both applications, quantification of PPIX forms the basis for accurate therapeutic dose calculation and identification of malignant tissues for resection. While it is well established that the PPIX synthesis and accumulation rates are subject to the cell's biochemical microenvironment, the effect of the physical microenvironment, such as matrix stiffness, has received little attention to date. Here we studied the proliferation rate and PPIX synthesis and accumulation in two glioma cell lines U373 and U118 cultured under five different substrate conditions, including the conventional tissue culture plastic and polyacrylamide gels that simulated tissue stiffness of normal brain (1 kPa) and glioblastoma tumors (12 kPa). We found that the proliferation rate increased with substrate stiffness for both cell lines, but not in a linear fashion. PPIX concentration was significantly higher in cells cultured on tissue-simulating gels than on the much stiffer tissue culture plastic for both cell lines. These findings, albeit preliminary, suggest that the physical microenvironment might be an important determinant of tumor aggressiveness and PPIX synthesis in glioma cells.

  19. Identification of Tuber borchii Vittad. mycelium proteins separated by two-dimensional polyacrylamide gel electrophoresis using amino acid analysis and sequence tagging.

    PubMed

    Vallorani, L; Bernardini, F; Sacconi, C; Pierleoni, R; Pieretti, B; Piccoli, G; Buffalini, M; Stocchi, V

    2000-11-01

    This paper reports the first results in the proteome analysis of Tuber borchii Vittad. mycelium, an ectomycorrhizal fungus poorly defined genetically, but known for its generation of edible fruit bodies known as white truffles. Employing isoelectric focusing on immobilized pH gradients, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, we obtained an electropherogram presenting over 800 spots within the window of isoelectric points (pI) 3.5-9 and a molecular mass of 10-200 kDa. Different reducing agents were tested in the sample preparation buffers, and the standard lysis buffer plus 2% w/v polyvinylpolypyrrolidone allowed the best solubilization and resolution of the proteins. The T. borchii proteins separated in micropreparative gels were electroblotted onto polyvinylidene difluoride membranes and visualized by Coomassie staining. Twenty-three proteins were excised and analyzed by the combination of amino acid and N-terminal analysis. One protein was identified by matching its amino acid composition, estimated isoelectric point and molecular mass against the SWISS-PROT and EMBL databases. Four spots were successfully tagged by Edman microsequencing but no homologous sequences were found in databases. PMID:11271490

  20. Rapid fluorescent monitoring of total protein patterns on sodium dodecyl sulfate-polyacrylamide gels and western blots before immunodetection and sequencing.

    PubMed

    Alba, F J; Daban, J R

    1998-10-01

    The fluorogenic dye 2-methoxy-2,4-diphenyl-3(2H)-furanone (MDPF) has been used for the detection of total protein patterns on polyvinylidene difluoride (PVDF) membranes. Fluorescent staining of protein bands on membranes with this covalent dye is completed in 20 min. Wet membranes are translucent, allowing protein visualization by transillumination with ultraviolet light. The resulting images can be recorded using Polaroid film or a charge-coupled device camera. Electrophoretic bands containing 5-10 ng of protein can be detected on the MDPF-stained Western blot. When proteins are directly transferred to the membrane using a slot blotting device, as little as 0.5 ng of protein can be detected. Previous visualization of protein bands on sodium dodecyl sulfate-polyacrylamide gels with the noncovalent fluorescent dye Nile red (Alba et al., BioTechniques, 1996, 21, 625-626) does not interfere with further MDPF staining and fluorescent detection of these bands transferred to PVDF membranes. Thus, Nile red and MDPF staining can be performed sequentially, allowing the rapid monitoring of total protein patterns on both the electrophoretic gel and Western blot. Using the conditions described in this study, MDPF staining does not preclude further N-terminal microsequencing and immunodetection of specific bands with polyclonal antibodies. PMID:9820958

  1. 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.

  2. A rapid and simple 8-quinolinol-based fluorescent stain of phosphoproteins in polyacrylamide gel after electrophoresis.

    PubMed

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

    2015-10-01

    In order to obtain an easy and rapid protocol to visualize phosphoproteins in SDS-PAGE, a fluorescent detection method named 8-Quinolinol (8-Q) stain is described. 8-Q can form ternary complexes in the gel matrix contributed by the affinity of aluminum ion (Al(3+) ) to the phosphate groups on the proteins and the metal chelating property of 8-Quinolinol, exhibiting strong fluorescence in ultraviolet light. It can visualize as little as 4∼8 ng of α-casein and β-casein, 16∼32 ng of ovalbumin and κ-casein which is more sensitive than Stains-All but less sensitive than Pro-Q Diamond. The protocol of 8-Q requires only 70 min in 0.75 mm mini-size or 1.0 mm large-size gels with five changes of solutions without destaining step; Pro-Q takes at least 250 min with 11 changes of solutions. In addition, the new method was confirmed by the study of dephosphorylation and LC-MS/MS, respectively. The approach to visualize phosphoprotein utilizing 8-Q could be an alternative to simplify the analytical operations for phosphoproteomics research. PMID:26177935

  3. 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

  4. Coordination mechanism, characterization, and photoluminescence properties of spinel ZnAl2O4 nanoparticles prepared by a modified polyacrylamide gel route

    NASA Astrophysics Data System (ADS)

    Sun, Guangzhuang; Sun, Guangai; Zhong, Mian; Wang, Shifa; Zu, Xiaotao; Xiang, Xia

    2016-03-01

    Single-phase ZnAl2O4 nanoparticles with the spinel structure were successfully synthesized using a modified polyacrylamide gel method according to the atomic ratio of Zn to Al = 1: 1.8. The as-prepared samples were characterized by means of X-ray powder diffraction (XRD), thermogravimetric analysis (TG), differential scanning calorimetry analysis (DSC), field-emission scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and photoluminescence (PL) spectra. XRD patterns show that the pure phase of ZnAl2O4 is obtained after heating the xerogel at 900°C for 5 h in air. The SEM images reveal that the ZnAl2O4 nanoparticles have a narrow particle size distribution and the average particle size is around 45 nm. Photoluminescence (PL) spectra demonstrate the single phase ZnAl2O4 nanoparticles have an emission peak located at 469 nm when excited by 350 nm light. The phase structure, coordination mechanism, and luminescence properties have been discussed on the basis of the experimental results.

  5. Fabrication of a novel light emission material AlFeO3 by a modified polyacrylamide gel route and characterization of the material

    NASA Astrophysics Data System (ADS)

    Wang, Shi-Fa; Zhang, Chuanfei; Sun, Guangai; Chen, Bo; Xiang, Xia; Wang, Hong; Fang, Leiming; Tian, Qiang; Ding, Qingping; Zu, XiaoTao

    2013-12-01

    AlFeO3 powders have been prepared by a modified polyacrylamide gel method and their thermal expansion and photoluminescence properties have been studied for the first time. The phase, morphology and thermal expansion behavior of as-prepared samples were analyzed via X-ray diffraction (XRD), Scanning electron microscope (SEM), and thermal dilatometer. XRD analysis indicates that the as-synthesized AlFeO3 has the same structure as α-Fe2O3 without the presence of any other impurities. SEM observation shows that the morphology of AlFeO3 powder is significantly dependent on the sintering temperature. The thermal expansion and differential scanning calorimetry (DSC) curves of AlFeO3 sample analysis indicates that a phase transition near 700 °C. The crystal growth mechanisms, coordination mechanisms, phase transformation process and luminescence mechanisms of AlFeO3 have been discussed on the basis of the experimental results. The blue light emission at 2.76 eV is due to intracenter 4T1 → 6A1 transitions in Fe3+ ions.

  6. Rapid and simple profiling of lipoproteins by polyacrylamide-gel disc electrophoresis to determine the heterogeneity of low-density lipoproteins (LDLs) including small, dense LDL.

    PubMed

    Nakano, Takanari; Inoue, Ikuo; Seo, Makoto; Takahashi, Seiichiro; Awata, Takuya; Komoda, Tsugikazu; Katayama, Shigehiro

    2009-01-01

    This study aimed to explore the potential of polyacrylamide-gel disc electrophoresis (PAGE) for lipoprotein profiling in clinical practice. Blood samples were collected from 146 patients with type 2 diabetes mellitus and lipid parameters were assayed by PAGE, including small, dense low-density lipoprotein (LDL) (n = 41), and triglyceride-rich lipoprotein remnant cholesterol (n = 37). We also used a commercial kit to measure small, dense LDL (n = 41). By PAGE, we obtained the percentage of the area under the curve (AUC %) of each peaks and calculated respective AUC% x total cholesterol (AUC%xTC) values. The calculated values of LDL-AUC%xTC, small LDL-AUC%xTC, and HDL-AUC%xTC values were correlated well with values from homogeneous assay for LDL-cholesterol, small, dense LDL-cholesterol, and HDL-cholesterol assays (r = 0.94, 0.81, and 0.89, respectively). PAGE combined with measurement of total cholesterol and triglycerides provides a rapid evaluation of anti- or pro-atherogenic lipoproteins and a simple profiling system for both the "quantity" and "quality" of lipoproteins, allowing a better assessment of the risk of coronary artery diseases. This article discusses several methods for simple and rapid lipid profiling and outlines some recent patents relevant to the methods. PMID:19149704

  7. Characterization of beta-lactoglobulin fibrillar assembly using atomic force microscopy, polyacrylamide gel electrophoresis, and in situ fourier transform infrared spectroscopy.

    PubMed

    Oboroceanu, Daniela; Wang, Lizhe; Brodkorb, André; Magner, Edmond; Auty, Mark A E

    2010-03-24

    The aggregation process of beta-lactoglobulin (beta-lg) from 0 min to 20 h was studied using atomic force microscopy (AFM), scanning transmission electron microscopy (STEM), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and in situ attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). Fibril assembly was monitored in real time using AFM up to 20 h. From 0 to 85 min, beta-lg monomers deformed and expanded with some aggregation. After 85 min, fibrillar structures were formed, exceeding 10 mum in length. Fibrillar structures were confirmed by STEM. Secondary structural changes occurring during fibril formation were monitored by ATR-FTIR at 80 degrees C and indicated a decrease in alpha-helix content and an increase in beta-sheet content. SDS-PAGE indicated that fibrils were composed of polypeptides and not intact monomers. In this study, beta-lg and whey protein isolate (WPI)-derived fibrils, including some double helices, in water were observed by AFM under ambient conditions and in their native aqueous environment. PMID:20187607

  8. Comparison of sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles and antigenic relatedness among outer membrane proteins of 49 Brucella abortus strains.

    PubMed Central

    Verstreate, D R; Winter, A J

    1984-01-01

    Outer membrane proteins were solubilized from 49 strains of Brucella abortus by sequential extraction of physically disrupted cells with N-lauroylsarcosinate and a dipolar ionic detergent (Verstreate et al., Infect. Immun. 35:979-989, 1982). The strains tested included standard agglutination test strain 1119, virulent strain 2308, and eight reference strains representing each of the biotypes; the remainder were isolates from cattle in North America with natural infections and included biotypes 1, 2, and 4. Three principal protein groups with apparent molecular weights of 88,000 to 94,000 (group 1), 35,000 to 40,000 (group 2, now established as porins [Douglas et al., Infect. Immun. 44:16-21, 1984]), and 25,000 to 30,000 (group 3) were observed in every strain. Some variability in banding patterns occurred among strains, but intrastrain variation was sufficient to preclude the use of sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles of outer membrane proteins for differentiating among strains of B. abortus. One antigen ([b]) was shared among the porin proteins, and three others ([c], ([d], and ([ e]) were shared among the group 3 proteins of all of the strains tested, indicating that these relationships are probably species wide. These results suggest that it may be possible to use outer membrane proteins from a representative strain of B. abortus in a vaccine for species-wide immunization. Images PMID:6434426

  9. Structural Studies of Avian Myeloblastosis Virus: Comparison of Polypeptides in Virion and Core Component by Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis

    PubMed Central

    Stromberg, Kurt; Hurley, Nancy E.; Davis, Nancy L.; Rueckert, Roland R.; Fleissner, Erwin

    1974-01-01

    Two different systems of dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in separate laboratories detected analogous patterns of dye bands in virions of avian myeloblastosis virus (AMV). At least 11 of the dye bands co-migrated with the major polypeptides reported in Rous sarcoma virus. Particles with the morphology of the AMV core component, obtained after exposure of AMV to the nonionic surfactant Sterox SL, contained major polypeptides p12, p27, p60, p64, p91, and p98. The polypeptide p12 has been previously shown to be the major constituent of the inner ribonucleoprotein (RNP) of the AMV core, and has been designated p12(N). Two RNP polypeptides, p64 and p91, co-electrophoresed with purified AMV DNA polymerase and have now been designated p64(P) and p91(P). The polypeptide p27 has been identified as a probable constituent of the core shell, and has accordingly now been designated p27(C). In comparison to virions of AMV, the AMV core component contained a greatly reduced amount of polypeptide p15 and appeared to lack a major polypeptide, p19. Consequently, these polypeptides may be associated either with the exterior of the core shell or the interior of the viral envelope. Glycopeptides were not detected in AMV cores, in agreement with earlier reports that they reside in external projections from the viral envelope. Images PMID:4129794

  10. Analysis of rRNA Gene Methylation in Arabidopsis thaliana by CHEF-Conventional 2D Gel Electrophoresis.

    PubMed

    Mohannath, Gireesha; Pikaard, Craig S

    2016-01-01

    Contour-clamped homogenous electric field (CHEF) gel electrophoresis, a variant of Pulsed-field gel electrophoresis (PFGE), is a powerful technique for resolving large fragments of DNA (10 kb-9 Mb). CHEF has many applications including the physical mapping of chromosomes, artificial chromosomes, and sub-chromosomal DNA fragments, etc. Here, we describe the use of CHEF and two-dimensional gel electrophoresis to analyze rRNA gene methylation patterns within the two ~4 million base pair nucleolus organizer regions (NORs) of Arabidopsis thaliana. The method involves CHEF gel electrophoresis of agarose-embedded DNA following restriction endonuclease digestion to cut the NORs into large but resolvable segments, followed by digestion with methylation-sensitive restriction endonucleases and conventional (or CHEF) gel electrophoresis, in a second dimension. Resulting products are then detected by Southern blotting or PCR analyses capable of discriminating rRNA gene subtypes. PMID:27576719

  11. Fluorescent staining of glycoproteins in sodium dodecyl sulfate polyacrylamide gels by 4H-[1]-benzopyrano[4,3-b]thiophene-2-carboxylic acid hydrazide.

    PubMed

    Zhu, Zhongxin; Zhou, Xuan; Wang, Yang; Chi, Lisha; Ruan, Dandan; Xuan, Yuanhu; Cong, Weitao; Jin, Litai

    2014-06-01

    A fluorescent detection method for glycoproteins in SDS-PAGE by using 4H-[1]-benzopyrano[4,3-b]thiophene-2-carboxylic acid hydrazide (BH) was developed in this study. As low as 4-8 ng glycoproteins (transferrin, α1-acid glycoprotein) could be specifically detected by the BH staining method, which is twofold more sensitive than that of the most commonly used Pro-Q Emerald 488 glycoprotein stain. Furthermore, the specificity of the newly developed stain for glycoproteins was demonstrated by 1-D and 2-D SDS-PAGE, deglycosylation, glycoprotein affinity enrichment and LC-MS/MS, respectively. According to the results, it is concluded that BH stain may provide new choices for convenient, sensitive, specific and economic visualization of gel-separated glycoproteins. PMID:24712021

  12. Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome

    PubMed Central

    2009-01-01

    The in vitro stationary phase proteome of the human pathogen Shigella dysenteriae serotype 1 (SD1) was quantitatively analyzed in Coomassie Blue G250 (CBB)-stained 2D gels. More than four hundred and fifty proteins, of which 271 were associated with distinct gel spots, were identified. In parallel, we employed 2D-LC-MS/MS followed by the label-free computationally modified spectral counting method APEX for absolute protein expression measurements. Of the 4502 genome-predicted SD1 proteins, 1148 proteins were identified with a false positive discovery rate of 5% and quantitated using 2D-LC-MS/MS and APEX. The dynamic range of the APEX method was approximately one order of magnitude higher than that of CBB-stained spot intensity quantitation. A squared Pearson correlation analysis revealed a reasonably good correlation (R2 = 0.67) for protein quantities surveyed by both methods. The correlation was decreased for protein subsets with specific physicochemical properties, such as low Mr values and high hydropathy scores. Stoichiometric ratios of subunits of protein complexes characterized in E. coli were compared with APEX quantitative ratios of orthologous SD1 protein complexes. A high correlation was observed for subunits of soluble cellular protein complexes in several cases, demonstrating versatile applications of the APEX method in quantitative proteomics. PMID:19563668

  13. Definition of Mycobacterium tuberculosis culture filtrate proteins by two-dimensional polyacrylamide gel electrophoresis, N-terminal amino acid sequencing, and electrospray mass spectrometry.

    PubMed Central

    Sonnenberg, M G; Belisle, J T

    1997-01-01

    A number of the culture filtrate proteins secreted by Mycobacterium tuberculosis are known to contribute to the immunology of tuberculosis and to possess enzymatic activities associated with pathogenicity. However, a complete analysis of the protein composition of this fraction has been lacking. By using two-dimensional polyacrylamide gel electrophoresis, detailed maps of the culture filtrate proteins of M. tuberculosis H37Rv were generated. In total, 205 protein spots were observed. The coupling of this electrophoretic technique with Western blot analysis allowed the identification and mapping of 32 proteins. Further molecular characterization of abundant proteins within this fraction was achieved by N-terminal amino acid sequencing and liquid chromatography-mass spectrometry. Eighteen proteins were subjected to N-group analysis; of these, only 10 could be sequenced by Edman degradation. Among the most interesting were a novel 52-kDa protein demonstrating significant homology to an alpha-hydroxysteroid dehydrogenase of Eubacterium sp. strain VPI 12708, a 25-kDa protein corresponding to open reading frame 28 of the M. tuberculosis cosmid MTCY1A11, and a 31-kDa protein exhibiting an amino acid sequence identical to that of antigen 85A and 85B. This latter product migrated with an isoelectric point between those of antigen 85A and 85C but did not react with the antibody specific for this complex, suggesting that there is a fourth member of the antigen 85 complex. Novel N-terminal amino acid sequences were obtained for three additional culture filtrate proteins; however, these did not yield significant homology to known protein sequences. A protein cluster of 85 to 88 kDa, recognized by the monoclonal antibodies IT-57 and IT-42 and known to react with sera from a large proportion of tuberculosis patients, was refractory to N-group analysis. Nevertheless, mass spectrometry of peptides obtained from one member of this complex identified it as the M. tuberculosis Kat

  14. Determination of optimal protein quantity required to identify abundant and less abundant soybean seed proteins by 2D-PAGE and MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Optimizing the amounts of proteins required to separate and characterize both abundant and less abundant proteins by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is critical for conducting proteomic research. In this study, we tested five different levels of soybean seed proteins (7...

  15. Single-step electrotransfer of reverse-stained proteins from sodium dodecyl sulfate-polyacrylamide gel onto reversed-phase minicartridge and subsequent desalting and elution with a conventional high-performance liquid chromatography gradient system for analysis.

    PubMed

    Fernandez-Patron, C; Madrazo, J; Hardy, E; Mendez, E; Frank, R; Castellanos-Serra, L

    1995-06-01

    Isolation of proteins from polyacrylamide electrophoresis gels by a novel combination of techniques is described. A given protein band from a reverse stained (imidazol-sodium dodecyl sulfate--zinc salts) gel can be directly electrotransferred onto a reversed-phase chromatographic support, packed in a self-made minicartridge (2 mm in thickness, 8 mm in internal diameter, made of inert polymeric materials). The minicartridge is then connected to a high-performance liquid chromatography system and the electrotransferred protein eluted by applying an acetonitrile gradient. Proteins elute in a small volume ( < 700 microL) of high-purity volatile solvents (water, trifluoroacetic acid, acetonitrile) and are free of contaminants (gel contaminants, salts, etc). Electrotransferred proteins were efficiently retained, e.g., up to 90% for radioiodinated alpha-lactalbumin, by the octadecyl matrix, and their recovery on elution from the minicartridge was in the range typical for this type of chromatographic support, e.g., 73% for alpha-lactalbumin. The technique was successfully applied to a variety of proteins in the molecular mass range 6-68 kDa, and with amounts between 50 and 2000 pmol. The good mechanical and chemical stability of the developed minicartridges, during electrotransfer and chromatography, allowed their repeated use. This new technique permitted a single-step separation of two proteins unresolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis due to their different elution from the reversed-phase support. The isolated proteins were amenable to analysis by N-terminal sequencing, enzymic digestion and mass spectrometry of their proteolytic fragments. Chromatographic elution of proteins from the reversed-phase mini-cartridge was apparently independent of the specific loading mode employed, i.e., loading by conventional loop injection or by electrotransfer. PMID:7498136

  16. A quantitative analysis of 2-D gels identifies proteins in which labeling is increased following long-term sensitization in Aplysia

    SciTech Connect

    Castellucci, V.F.; Kennedy, T.E.; Kandel, E.R.; Goelet, P. )

    1988-06-01

    Long-term memory for sensitization of the gill- and siphon-withdrawal reflex in Aplysia, produced by 4 days of training, is associated with increased synaptic efficacy of the connection between the sensory and motor neurons. This training is also accompanied by neuronal growth; there is an increase in the number of synaptic varicosities per sensory neuron and in the number of active zones. Such structural changes may be due to changes in the rates of synthesis of certain proteins. We have searched for proteins in which the rates of ({sup 35}S)methionine labeling are altered during the maintenance phase of long-term memory for sensitization by using computer-assisted quantitative 2-D gel analysis. This method has allowed us to detect 4 proteins in which labeling is altered after 4 days of sensitization training.

  17. Profiling of myelin proteins by 2D-gel electrophoresis and multidimensional liquid chromatography coupled to MALDI TOF-TOF mass spectrometry.

    PubMed

    Vanrobaeys, Frank; Van Coster, Rudy; Dhondt, Goedele; Devreese, Bart; Van Beeumen, Jozef

    2005-01-01

    The myelin sheath is an electrically insulating layer that consists of lipids and proteins. It plays a key role in the functioning of the nervous system by allowing fast saltatory conduction of nerve pulses. Profiling of the proteins present in myelin is an indispensable prerequisite to better understand the molecular aspects of this dynamic, functionally active membrane. Two types of protein, the myelin basic protein and the proteolipid protein, account for nearly 85% of the protein content in myelin. Identification and characterization of the other "minor" proteins is, in this respect, a real challenge. In the present work, two proteomic strategies were applied in order to study the protein composition of myelin from the murine central nervous system. First, the protein mixture was separated by 2D-gel electrophoresis and, after spot excision and in-gel digestion, samples were analyzed by mass spectrometry. Via this approach, we identified 57 protein spots, corresponding to 38 unique proteins. Alternatively, the myelin sample was digested by trypsin and the resulting peptide mixture was further analyzed by off-line 2D-liquid chromatography. After the second-dimension separation (nanoLC), the peptides were spotted "on-line" onto a MALDI target and analyzed by MALDI TOF-TOF mass spectrometry. We identified 812 peptides by MALDI MS/MS, representing 93 proteins. Membrane proteins, low abundant proteins, and highly basic proteins were all represented in this shotgun proteomic approach. By combining the results of both approaches, we can present a comprehensive proteomic map of myelin, comprising a total of 103 protein identifications, which is of utmost importance for the molecular understanding of white matter and its disorders. PMID:16335977

  18. Identification of 2D-gel proteins : a comparison of MALDI/TOF peptide mass mapping to {mu} LC-ESI tandem mass spectrometry.

    SciTech Connect

    Lim, H.; Hays, L. G.; Eng, J.; Tollaksen, S. L.; Giometti, C. S.; Holden, J. F.; Adams, M. W. W.; Reich, C. I.; Olsen, G. J.; Yates, J. R.; Biosciences Division; The Scripps Research Inst.; Univ. of Georgia; Univ. of Illinois

    2003-09-01

    A comparative analysis of protein identification for a total of 162 protein spots separated by two-dimensional gel electrophoresis from two fully sequenced archaea, Methanococcus jannaschii and Pyrococcus furiosus, using MALDI-TOF peptide mass mapping (PMM) and mu LC-MS/MS is presented. 100% of the gel spots analyzed were successfully matched to the predicted proteins in the two corresponding open reading frame databases by mu LC-MS/MS while 97% of them were identified by MALDI-TOF PMM. The high success rate from the PMM resulted from sample desalting/concentrating with ZipTip(C18) and optimization of several PMM search parameters including a 25 ppm average mass tolerance and the application of two different protein molecular weight search windows. By using this strategy, low-molecular weight (<23 kDa) proteins could be identified unambiguously with less than 5 peptide matches. Nine percent of spots were identified as containing multiple proteins. By using mu LC-MS/MS, 50% of the spots analyzed were identified as containing multiple proteins. mu LC-MS/MS demonstrated better protein sequence coverage than MALDI-TOF PMM over the entire mass range of proteins identified. MALDI-TOF and PMM produced unique peptide molecular weight matches that were not identified by mu LC-MS/MS. By incorporating amino acid sequence modifications into database searches, combined sequence coverage obtained from these two complimentary ionization methods exceeded 50% for approximately 70% of the 162 spots analyzed. This improved sequence coverage in combination with enzymatic digestions of different specificity is proposed as a method for analysis of post-translational modification from 2D-gel separated proteins.

  19. Analysis of soybean embryonic axis proteins by two-dimensional gel electrophoresis and mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A proteomic approach based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for protein separation and subsequent mass spectrometry (MS) for protein identification was applied to establish a proteomic reference map for the soybean embryonic axis. Proteins were extracted from dissecte...

  20. Region-based Statistical Analysis of 2D PAGE Images

    PubMed Central

    Li, Feng; Seillier-Moiseiwitsch, Françoise; Korostyshevskiy, Valeriy R.

    2011-01-01

    A new comprehensive procedure for statistical analysis of two-dimensional polyacrylamide gel electrophoresis (2D PAGE) images is proposed, including protein region quantification, normalization and statistical analysis. Protein regions are defined by the master watershed map that is obtained from the mean gel. By working with these protein regions, the approach bypasses the current bottleneck in the analysis of 2D PAGE images: it does not require spot matching. Background correction is implemented in each protein region by local segmentation. Two-dimensional locally weighted smoothing (LOESS) is proposed to remove any systematic bias after quantification of protein regions. Proteins are separated into mutually independent sets based on detected correlations, and a multivariate analysis is used on each set to detect the group effect. A strategy for multiple hypothesis testing based on this multivariate approach combined with the usual Benjamini-Hochberg FDR procedure is formulated and applied to the differential analysis of 2D PAGE images. Each step in the analytical protocol is shown by using an actual dataset. The effectiveness of the proposed methodology is shown using simulated gels in comparison with the commercial software packages PDQuest and Dymension. We also introduce a new procedure for simulating gel images. PMID:21850152

  1. Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5†

    PubMed Central

    Ralph, John

    2014-01-01

    NMR fingerprinting of the components of finely divided plant cell walls swelled in DMSO has been recently described. Cell wall gels, produced directly in the NMR tube with perdeutero-dimethylsulfoxide, allowed the acquisition of well resolved/dispersed 2D 13C–1H correlated solution-state NMR spectra of the entire array of wall polymers, without the need for component fractionation. That is, without actual solubilization, and without apparent structural modification beyond that inflicted by the ball milling and ultrasonication steps, satisfactorily interpretable spectra can be acquired that reveal compositional and structural details regarding the polysaccharide and lignin components in the wall. Here, the profiling method has been improved by using a mixture of perdeuterated DMSO and pyridine (4:1, v/v). Adding pyridine provided not only easier sample handling because of the better mobility compared to the DMSO-d6-only system but also considerably elevated intensities and improved resolution of the NMR spectra due to the enhanced swelling of the cell walls. This modification therefore provides a more rapid method for comparative structural evaluation of plant cell walls than is currently available. We examined loblolly pine (Pinus taeda, a gymnosperm), aspen (Populus tremuloides, an angiosperm), kenaf (Hibiscus cannabinus, an herbaceous plant), and corn (Zea mays L., a grass, i.e., from the Poaceae family). In principle, lignin composition (notably, the syringyl : guaiacyl : p-hydroxyphenyl ratio) can be quantified without the need for lignin isolation. Correlations for p-coumarate units in the corn sample are readily seen, and a variety of the ferulate correlations are also well resolved; ferulates are important components responsible for cell wall cross-linking in grasses. Polysaccharide anomeric correlations were tentatively assigned for each plant sample based on standard samples and various literature data. With the new potential for chemometric analysis

  2. 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

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

    1997-10-01

    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

  3. [Urine protein analysis with the sodium-dodecyl-sulfate-polyacrylamide gel-electrophoresis (SDS-PAGE) in healthy cats and cats with kidney diseases].

    PubMed

    Meyer-Lindenberg, A; Wohlsein, P; Trautwein, G; Nolte, I

    1997-03-01

    In this investigation, the value of urine protein analysis by means of molecular-weight related sodium dodecyl-polyacryl gradient gel electrophoresis (SDS-PAGE) was examined with regard to its applicability and diagnostic significance in nephropathy in the cat. A total of 87 cats was included in the study, 30 of them that were clinically healthy served as the control group. The urine protein pattern of this group had, besides the band representing the market albumin, and additional broad band within the size of the marker transferrin. In some cases, weak bands were present within the range of the Tamm-Horsfall-protein and immunoglobulin G. Micromolecular protein bands were not demonstrable. The remaining 57 animals had a histologically proven nephropathy. Thirty-eight cats had elevated urea and/or creatinine values in the plasma (group 1), and 19 animals had values within the reference range (group 2). The urine protein pattern as evidenced by SDS-urine electrophoresis was altered in all cats with histologically proven nephropathy, and it is thus concluded that with this technique a nephropathy can be diagnosed very early and prior to changes of plasma urea and creatinine (group 2). Moreover, in most of the cases, the nephrological changes can be classified as glomerular or tubulo-interstitial (group 1 and group 2). However, it is not possible to draw exact conclusions concerning the underlying morphological changes, nor can the severity of the disease be correctly assessed. PMID:9123982

  4. Preparation of DNA-crosslinked polyacrylamide hydrogels.

    PubMed

    Previtera, Michelle L; Langrana, Noshir A

    2014-01-01

    Mechanobiology is an emerging scientific area that addresses the critical role of physical cues in directing cell morphology and function. For example, the effect of tissue elasticity on cell function is a major area of mechanobiology research because tissue stiffness modulates with disease, development, and injury. Static tissue-mimicking materials, or materials that cannot alter stiffness once cells are plated, are predominately used to investigate the effects of tissue stiffness on cell functions. While information gathered from static studies is valuable, these studies are not indicative of the dynamic nature of the cellular microenvironment in vivo. To better address the effects of dynamic stiffness on cell function, we developed a DNA-crosslinked polyacrylamide hydrogel system (DNA gels). Unlike other dynamic substrates, DNA gels have the ability to decrease or increase in stiffness after fabrication without stimuli. DNA gels consist of DNA crosslinks that are polymerized into a polyacrylamide backbone. Adding and removing crosslinks via delivery of single-stranded DNA allows temporal, spatial, and reversible control of gel elasticity. We have shown in previous reports that dynamic modulation of DNA gel elasticity influences fibroblast and neuron behavior. In this report and video, we provide a schematic that describes the DNA gel crosslinking mechanisms and step-by-step instructions on the preparation DNA gels. PMID:25226067

  5. Improved method for identification of low abundance proteins using 2D-gel electrophoresis, MALDI-TOF and TOF/TOF

    EPA Science Inventory

    Introduction: Differential protein expression studies have been routinely performed in our laboratory to determine the health effects of environmentally-important chemicals. In this abstract, improvements in the in-gel protein digestion, MALDI plate spotting and data acquisition...

  6. Protein imprinting in polyacrylamide-based gels

    PubMed Central

    Zayats, Maya; Brenner, Andrew J.; Searson, Peter C.

    2015-01-01

    Protein imprinting in hydrogels is a method to produce materials capable of selective recognition and capture of a target protein. Here we report on the imprinting of fluorescently-labeled maltose binding protein (MBP) in acrylamide (AAm)/N-isopropylacrylamide (NIPAm) hydrogels. The targeting efficiency and selectivity of protein recognition is usually characterized by the imprinting factor, which in the simplest case is the ratio of protein uptake in an imprinted film divided by the uptake by the corresponding non-imprinted film. Our objective in this work is to study the dynamics of protein binding and elution in imprinted and non-imprinted films to elucidate the processes that control protein recognition. Protein elution from imprinted and non-imprinted films suggests that imprinting results in sites with a distribution of binding energies, and that only a relatively small fraction of these sites exhibit strong binding. PMID:25034963

  7. Protein imprinting in polyacrylamide-based gels.

    PubMed

    Zayats, Maya; Brenner, Andrew J; Searson, Peter C

    2014-10-01

    Protein imprinting in hydrogels is a method to produce materials capable of selective recognition and capture of a target protein. Here we report on the imprinting of fluorescently-labeled maltose binding protein (MBP) in acrylamide (AAm)/N-isopropylacrylamide (NIPAm) hydrogels. The targeting efficiency and selectivity of protein recognition is usually characterized by the imprinting factor, which in the simplest case is the ratio of protein uptake in an imprinted film divided by the uptake by the corresponding non-imprinted film. Our objective in this work is to study the dynamics of protein binding and elution in imprinted and non-imprinted films to elucidate the processes that control protein recognition. Protein elution from imprinted and non-imprinted films suggests that imprinting results in sites with a distribution of binding energies, and that only a relatively small fraction of these sites exhibit strong binding. PMID:25034963

  8. 2DBase: 2D-PAGE database of Escherichia coli.

    PubMed

    Vijayendran, Chandran; Burgemeister, Sebastian; Friehs, Karl; Niehaus, Karsten; Flaschel, Erwin

    2007-11-23

    We present a web-based integrated proteome database, termed 2DBase of Escherichia coli which was designed to store, compare, analyse, and retrieve various information obtained by 2D polyacrylamide gel electrophoresis and mass spectrometry. The main objectives of this database are (1) to provide the features for query and data-mining applications to access the stored proteomics data (2) to efficiently compare the specific protein spots present in the comparable proteome maps and (3) to analyse the data with the integrated classification for cellular functions of gene products of E. coli. This database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins were identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analyzed, and compared in a tabular format based on various functional categories enabling quick and subsequent analyses. Our database satisfies the requirement to be a federated 2-DE database by accomplishing various tasks through a web interface providing access to a relational database system. The 2DBase of E. coli database can be accessed at http://2dbase.techfak.uni-bielefeld.de/. PMID:17904107

  9. A vertical submarine electrophoresis apparatus for polyacrylamide minigels.

    PubMed

    Spiker, S

    1990-03-01

    A vertical submarine electrophoresis apparatus for use with minislab polyacrylamide gels is described. The design allows polyacrylamide gels to be run with the same ease and convenience that agarose gels are run with horizontal submarine apparatuses. The vertical submarine features a single buffer chamber with a restriction between the upper and the lower portions of the chamber. Acrylamide gels, cast between 9 X 10-cm glass slides, are inserted into the restriction and are completely immersed in buffer. Thus, current flows primarily through the gel itself, but some current flows through the buffer in the restriction surrounding the gel. Because water-tight separation of buffer chambers is not necessary, time-consuming and/or expensive procedures such as sealing with agarose or using fragile notched glass plates are eliminated. The apparatus can be set up to run a gel in less than 30 s. It is versatile in that gels of varying thickness (0.5, 0.8, 1.5, and 3 mm) can be run on a single apparatus. The apparatus has been used for sodium dodecyl sulfate gels, low ionic strength native gels for nucleoprotein complexes, and composite acrylamide-agarose gels. PMID:2339782

  10. Ocular Proteomics with Emphasis on Two-Dimensional Gel Electrophoresis and Mass Spectrometry

    PubMed Central

    2010-01-01

    The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC) are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions. PMID:21406065

  11. Proteomic analysis by two-dimensional differential in gel electrophoresis (2D DIGE) of the early response of Pisum sativum to Orobanche crenata.

    PubMed

    Castillejo, Ma Ángeles; Fernández-Aparicio, Mónica; Rubiales, Diego

    2012-01-01

    Crenate broomrape (Orobanche crenata) is considered to be the major constraint for legume crops in Mediterranean countries. Strategies of control have been developed, but only marginal successes have been achieved. For the efficient control of the parasite, a better understanding of its interaction and associated resistance mechanisms at the molecular level is required. The pea response to this parasitic plant and the molecular basis of the resistance was studied using a proteomic approach based on 2D DIGE and MALDI-MSMS analysis. For this purpose, two genotypes showing different levels of resistance to O. crenata, as well as three time points (21, 25, and 30 d after inoculation) have been compared. Multivariate statistical analysis identified 43 differential protein spots under the experimental conditions (genotypes/treatments), 22 of which were identified using a combination of peptide mass fingerprinting (PMF) and MSMS fragmentation. Most of the proteins identified were metabolic and stress-related proteins and a high percentage of them (86%) matched with specific proteins of legume species. The behaviour pattern of the identified proteins suggests the existence of defence mechanisms operating during the early stages of infection that differed in both genotypes. Among these, several proteins were identified with protease activity which could play an important role in preventing the penetration and connection to the vascular system of the parasite. Our data are discussed and compared with those previously obtained in pea and Medicago truncatula. PMID:21920908

  12. Effect of cationic polyacrylamide on the processing and properties of nanocellulose films.

    PubMed

    Raj, Praveena; Varanasi, Swambabu; Batchelor, Warren; Garnier, Gil

    2015-06-01

    The use of high molecular weight cationic polyacrylamide (CPAM) was investigated to accelerate the drainage of nanocellulose (Microfibrillated Cellulose) suspensions into films. The mechanism was quantified and optimized by measuring the gel point, the lowest solids concentration at which a continuous network is formed. The flocculation of MFC was analysed as a function of the polyelectrolyte dosage, charge density and molecular weight as well as process parameters (drainage time) and material properties. The adsorption isotherms of CPAMs on nanocellulose and their zeta potential curves were also analysed as a function of CPAM charge and dosage. Measured CPAM adsorption capacities for the 50% and 10% charged 13MDa CPAM onto MFC were 5mg/g and 8mg/g, respectively, corresponding to adsorption coverage on cellulose of 0.14mg/m(2) and 0.22mg/m(2). The floc strength and drainability of MFC suspensions were quantified with the gel point as a function of CPAM properties. For all combinations of polyelectrolyte molecular weight and charge density, the gel point of a nanocellulose suspension goes through a minimum with increasing polymer dosage. The minimum gel point was independent of the polyelectrolyte charge density at constant molecular weight. However, it reduced with decreasing CPAM molecular weight, at a constant addition rate. The drainage time of a nanocellulose suspension into a film is reduced by 2/3 by halving the gel point from 0.2 to 0.1kg/m(3); this is due to the more flocculated suspension facilitating drainage between flocs. Nanocellulose films of increased porosity also result from reducing the gel point, signifying that the more open 3D structure of the flocculated cellulose suspension is retained upon drying the 2D film cellulose film structure. PMID:25702868

  13. A relational Fuzzy C-Means algorithm for detecting protein spots in two-dimensional gel images.

    PubMed

    Rashwan, Shaheera; Faheem, Talaat; Sarhan, Amany; Youssef, Bayumy A B

    2010-01-01

    Two-dimensional polyacrylamide gel electrophoresis of proteins is a robust and reproducible technique. It is the most widely used separation tool in proteomics. Current efforts in the field are directed at the development of tools for expanding the range of proteins accessible with two-dimensional gels. Proteomics was built around the two-dimensional gel. The idea that multiple proteins can be analyzed in parallel grew from two-dimensional gel maps. Proteomics researchers needed to identify interested protein spots by examining the gel. This is time consuming, labor extensive and error prone. It is desired that the computer can analyze the proteins automatically by first detecting, then quantifying the protein spots in the 2D gel images. This paper focuses on the protein spot detection and segmentation of 2D gel electrophoresis images. We present a new technique for segmentation of 2D gel images using the Fuzzy C-Means (FCM) algorithm and matching spots using the notion of fuzzy relations. Through the experimental results, the new algorithm was found out to detect protein spots more accurately, then the current known algorithms. PMID:20865504

  14. 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.

  15. 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.

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. Magnetic and spectroscopic properties of Polyacrylamide-CoFe2O4 magnetic hydrogel

    NASA Astrophysics Data System (ADS)

    Alveroğlu, E.; Sözeri, H.; Kurtan, U.; Şenel, M.; Baykal, A.

    2013-03-01

    This study investigates synthesis and characterization of polyacrylamide (PAAm) hydrogels containing ferromagnetic CoFe2O4 nanoparticles. Structural, electrical, and magnetic characterization of the gels have been performed with X-ray powder diffractometry, Scanning electron microscopy, DC conductivity, magnetization and fluorescence spectroscopy techniques. Fluorescence and electrical measurements show that nanoparticles have trapped in the gel so they cannot move through the gel even if the gel is swollen and the voltage is applied. Pyranine molecules diffuse easily through the gel due to the presence of ferromagnetic nanoparticles. As number of diffused pyranine molecules increases current densities of the magnetic hydrogel increase. Magnetization measurements reveal that CoFe2O4 nanoparticles do not diffuse out of the gel during swelling. As a result, total magnetization of the gel do not change as volume of the gel increases.

  1. Gel for Simultaneous Chemical Imaging of Anionic and Cationic Solutes Using Diffusive Gradients in Thin Films

    PubMed Central

    2013-01-01

    We report on a novel gel based on diffusive gradients in thin films (DGT) for the simultaneous measurement of cations and anions and its suitability for high resolution chemical imaging by using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). The new high resolution mixed binding gel (HR-MBG) is based on zirconium-hydroxide and suspended particulate reagent-iminodiacetate (SPR-IDA) as resin materials which are embedded in an ether-based urethane polymer hydrogel. The use of this polymer hydrogel material allows the production of ultrathin, highly stable and tear-proof resin gel layers with superior handling properties compared to existing ultrathin polyacrylamide gels. The gel was characterized regarding its uptake kinetics, the anion and cation capacities, and the effects of pH, ionic strength, and aging on the performance of the HR-MBG. Our results demonstrate the capability of this novel gel for concomitant sampling of anions and cations. The suitability of this new gel type for DGT chemical imaging at submm spatial resolution in soils using LA-ICPMS is shown. 2D images of P, As, Co, Cu, Mn, and Zn distributions around roots of Zea mays L. demonstrate the new opportunities offered by the HR-MBG for high-resolution mapping of solute dynamics in soil and sediment hotspots, such as the rhizosphere, by simultaneous observation of anionic and cationic solute species. PMID:24256092

  2. Gel for simultaneous chemical imaging of anionic and cationic solutes using diffusive gradients in thin films.

    PubMed

    Kreuzeder, Andreas; Santner, Jakob; Prohaska, Thomas; Wenzel, Walter W

    2013-12-17

    We report on a novel gel based on diffusive gradients in thin films (DGT) for the simultaneous measurement of cations and anions and its suitability for high resolution chemical imaging by using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). The new high resolution mixed binding gel (HR-MBG) is based on zirconium-hydroxide and suspended particulate reagent-iminodiacetate (SPR-IDA) as resin materials which are embedded in an ether-based urethane polymer hydrogel. The use of this polymer hydrogel material allows the production of ultrathin, highly stable and tear-proof resin gel layers with superior handling properties compared to existing ultrathin polyacrylamide gels. The gel was characterized regarding its uptake kinetics, the anion and cation capacities, and the effects of pH, ionic strength, and aging on the performance of the HR-MBG. Our results demonstrate the capability of this novel gel for concomitant sampling of anions and cations. The suitability of this new gel type for DGT chemical imaging at submm spatial resolution in soils using LA-ICPMS is shown. 2D images of P, As, Co, Cu, Mn, and Zn distributions around roots of Zea mays L. demonstrate the new opportunities offered by the HR-MBG for high-resolution mapping of solute dynamics in soil and sediment hotspots, such as the rhizosphere, by simultaneous observation of anionic and cationic solute species. PMID:24256092

  3. 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.

  4. 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.

  5. Protein transfer through polyacrylamide hydrogel membranes polymerized in lyotropic phases.

    PubMed

    Monteiro, Michael J; Hall, Geoff; Gee, Sarah; Xie, Li

    2004-01-01

    A way to control the average pore size in cross-linked polyacrylamide-based membranes is by altering the ratio of cross-linker to acylamide monomer. Larger pore sizes are prepared with a minimum amount of cross-linker, resulting in membranes that are mechanically weak and have short lifetimes. The aim of this study was to prepare cross-linked polyacrylamide membranes with large pore sizes and with good mechanical integrity. The methodology was to carry out the polymerization in a template, formed from the self-aggregation of surfactant. Two surfactant templates were used, and their pore size was examined with proteins of different sizes. The surfactants chosen for this study were sodium dodecyl sulfate (SDS, ionic surfactant) and TERIC BL8 (nonionic surfactant), both of which have very different aggregation properties. The data showed that at 10% and greater of TERIC BL8, a very different and open gel structure is formed, in which the pore size was significantly increased. SDS seemed to have little effect on the pore size. The data suggests that the gel structures for both surfactants up to 4% (w/v) are similar and micellular, because SDS is known to favor a micelle structure. Above 4% (w/v), TERIC BL8 then goes through a change in its lyotropic phase, thus, producing membranes of a large pore size. In conclusion, the pore size and gel structure of polyacrylamide hydrogel membranes can be significantly increased using TERIC BL8 (nonionic) surfactant. This allows large-pore-size membranes with a high cross-link density and consequently high mechanical strength to be prepared for the separation of large biomolecules. PMID:15360267

  6. Breast cancer following augmentation mammaplasty with polyacrylamide hydrogel (PAAG) injection.

    PubMed

    Cheng, Ning-Xin; Liu, Li-Gang; Hui, Li; Chen, Yuan-Liang; Xu, Shi-Liang

    2009-07-01

    Polyacrylamide hydrogel (PAAG) as an implanted material for augmentation mammaplasty has been used for years in China. Many kinds of complications associated with PAAG use have been reported in the clinical literature. This report presents two cases of breast cancer occurring after injection of PAAG in augmented breasts. The delayed diagnosis and more aggressive disease due to PAAG injection should be cause for concern. It is very important to detect breast cancer early when it is covered by the induration of the injected gel and inflammation reaction after PAAG injection. PAAG injection for augmentation mammaplasty may affect the outcome of breast cancer diagnosis and prognosis. PMID:19156460

  7. Polyacrylamide hydrogel differences: getting rid of the confusion.

    PubMed

    Narins, Rhoda S; Schmidt, Richard

    2011-12-01

    Polymer hydrogels have been used for many years in European and Asian countries, and these products are often considered to be the same material in different packaging. This, however, is not the case. Performance and safety profiles depend on many factors including chemical and physical characteristics (including rheological properties), manufacturing process and control (cross linking, impurities, stability, etc.), injection technique, and interaction with surrounding tissues. Polyacrylamide hydrogel (PAAH) products, although often considered equal, have clear differences in composition, manufacturing, and injection technique as well as ability to interact with surrounding tissues, characteristics that determine the safety and effectiveness profiles of each of these gels. PMID:22134560

  8. Polyacrylamide phantom for self-actuating needle-tissue interaction studies.

    PubMed

    Datla, Naresh V; Konh, Bardia; Koo, Joe J Y; Choi, Daniel J W; Yu, Yan; Dicker, Adam P; Podder, Tarun K; Darvish, Kurosh; Hutapea, Parsaoran

    2014-01-01

    This study presents a polyacrylamide gel as a phantom material for needle insertion studies specifically developed for self-actuating needles to enhance the precise placement of needles in prostate. Bending of these self-actuating needles within tissue is achieved by Nitinol actuators attached to the needle body; however these actuators usually involve heating that can thermally damage the tissue surrounding the needles. Therefore, to develop and access feasibility of these needles, a polyacrylamide gel has been developed that mimics the thermal damage and mechanical properties of prostate tissue. Mechanical properties of the polyacrylamide gel was controlled by varying the concentrations of acrylamide monomer and N,N-methylene-bisacrylamide (BIS) cross-linker, and thermal sensitivity was achieved by adding bovine serum albumin (BSA) protein. Two polyacrylamide gels with different concentrations were developed to mimic the elastic modulus of the tissue. The two phantoms showed different rupture toughness and different deflection of bevel-tip needle. To study the thermal damage, a Nitinol wire was embedded in the phantom and resistively heated. The measured opaque zone (0.40mm) formed around the wire was close to the estimated damage zone (0.43mm) determined using the cumulative equivalent minutes at 43°C. PMID:23932314

  9. 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…

  10. Aniso2D

    2005-07-01

    Aniso2d is a two-dimensional seismic forward modeling code. The earth is parameterized by an X-Z plane in which the seismic properties Can have monoclinic with x-z plane symmetry. The program uses a user define time-domain wavelet to produce synthetic seismograms anrwhere within the two-dimensional media.

  11. Simple polyacrylamide-based multiwell stiffness assay for the study of stiffness-dependent cell responses.

    PubMed

    Syed, Sana; Karadaghy, Amin; Zustiak, Silviya

    2015-01-01

    Currently, most of the in vitro cell research is performed on rigid tissue culture polystyrene (~1 GPa), while most cells in the body are attached to a matrix that is elastic and much softer (0.1-100 kPa). Since such stiffness mismatch greatly affects cell responses, there is a strong interest in developing hydrogel materials that span a wide range of stiffness to serve as cell substrates. Polyacrylamide gels, which are inexpensive and cover the stiffness range of all soft tissues in the body, are the hydrogel of choice for many research groups. However, polyacrylamide gel preparation is lengthy, tedious, and only suitable for small batches. Here, we describe an assay which by utilizing a permanent flexible plastic film as a structural support for the gels, enables the preparation of polyacrylamide gels in a multiwell plate format. The technique is faster, more efficient, and less costly than current methods and permits the preparation of gels of custom sizes not otherwise available. As it doesn't require any specialized equipment, the method could be easily adopted by any research laboratory and would be particularly useful in research focused on understanding stiffness-dependent cell responses. PMID:25866916

  12. Evaluation du potentiel radiosensibilisateur ou radioprotecteur/antioxydant de quelques composes selectionnes par dosimetrie par gel de polyacrylamide et dosimetre de Fricke, et utilisation de la filamentation par impulsion laser infrarouge fenitoseconde comme un nouveau et puissant faisceau pour la radiotherapie du cancer

    NASA Astrophysics Data System (ADS)

    Meesat, Ridthee

    In radiation treatment, a sufficiently high radiation dose must be delivered to the tissue volumes containing the tumor cells while the lowest possible dose should be deposited in surrounding healthy tissue. We developed an original approach that is fast and easy to implement for the early assessment of the efficiency of radiation sensitizers and protectors. In addition, we characterized a new femtosecond laser pulse irradiation technique. We are able to deposit a considerable dose with a very high dose rate inside a well-controlled macroscopic volume without deposition of energy in front or behind the target volume. The radioprotective efficiency was measured by irradiation of the Fricke solution incorporating a compound under study and measuring the corresponding production of ferric ions G(Fe3+). The production of ferric ions is most sensitive to the radical species produced in the radiolysis of water. We studied experimentally and simulated with a full Monte-Carlo computer code the radiation-induced chemistry of Fricke/cystamine solutions. Results clearly indicate that the protective effect of cystamine originates from its radical-capturing ability, which allows this compound to compete with the ferrous ions for the various free radicals - especially ·OH radicals and H· atoms - formed during irradiation of the surrounding water. The sensitizing capacity of radiation sensitizers was measured by irradiation of a polyacrylamide gel (PAG) dosimeter incorporating a compound under study and measuring the corresponding increase in the gradient between spin-spin relaxation rate (R2) and absorbed dose. We measured an irradiation energy-dependent increase in R 2-dose sensitivity for halogenated compounds or a decrease for radioprotectors. Finally, we studied a novel laser irradiation method called "filamentation". We showed that this phenomenon results in an unprecedented deposition of energy and the dose rate thus achieved exceeds by orders of magnitude values

  13. Mesh2d

    SciTech Connect

    Greg Flach, Frank Smith

    2011-12-31

    Mesh2d is a Fortran90 program designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). The x(i) coordinates alone can be used to specify a one-dimensional grid. Because the x-coordinates vary only with the i index, a two-dimensional grid is composed in part of straight vertical lines. However, the nominally horizontal y(i,j0) coordinates along index i are permitted to undulate or otherwise vary. Mesh2d also assigns an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations.

  14. Mesh2d

    2011-12-31

    Mesh2d is a Fortran90 program designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). The x(i) coordinates alone can be used to specify a one-dimensional grid. Because the x-coordinates vary only with the i index, a two-dimensional grid is composed in part of straight vertical lines. However, the nominally horizontal y(i,j0) coordinates along index i are permitted to undulate or otherwise vary. Mesh2d also assignsmore » an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations.« less

  15. Vertical 2D Heterostructures

    NASA Astrophysics Data System (ADS)

    Lotsch, Bettina V.

    2015-07-01

    Graphene's legacy has become an integral part of today's condensed matter science and has equipped a whole generation of scientists with an armory of concepts and techniques that open up new perspectives for the postgraphene area. In particular, the judicious combination of 2D building blocks into vertical heterostructures has recently been identified as a promising route to rationally engineer complex multilayer systems and artificial solids with intriguing properties. The present review highlights recent developments in the rapidly emerging field of 2D nanoarchitectonics from a materials chemistry perspective, with a focus on the types of heterostructures available, their assembly strategies, and their emerging properties. This overview is intended to bridge the gap between two major—yet largely disjunct—developments in 2D heterostructures, which are firmly rooted in solid-state chemistry or physics. Although the underlying types of heterostructures differ with respect to their dimensions, layer alignment, and interfacial quality, there is common ground, and future synergies between the various assembly strategies are to be expected.

  16. Identification and characterization of the 2D6 and Mr 23,000 antigens on the plasma membrane of rat spermatozoa.

    PubMed Central

    Jones, R; Brown, C R

    1987-01-01

    Previous investigations [Jones, Brown, von Glos & Gaunt (1985) Exp. Cell Res. 156, 31-44] have demonstrated the appearance of a new antigenic determinant (recognized by monoclonal antibody 2D6) on the plasma membrane of rat spermatozoa during post-testicular maturation in the epididymis. Identification of the 2D6 antigen on Western blots from one-dimensional SDS/polyacrylamide gels revealed that it co-migrated with a membrane protein (designated Mr 23,000 antigen) present on testicular and immature germ cells, suggesting that one antigen might be a modified version of the other. In the present work, however, we demonstrate that, although they have similar Mr and are present in soluble and membrane-bound forms, the 2D6 and Mr 23,000 antigens are biochemically and immunologically distinct molecules. The properties of the antigens are described and compared. The Mr 23,000 antigen is present on both testicular and cauda epididymidal spermatozoa, has a pI of 6.1, contains no detectable carbohydrate, is not tissue-specific and is degraded by V8 protease. By contrast, the 2D6 antigen is glycosylated, has a broad pI from 4.5 to 6.1, is tissue- and species-specific and is resistant to digestion with V8 protease. Its role in sperm-egg recognition is discussed. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:2439064

  17. Pouring and running a protein gel by reusing commercial cassettes.

    PubMed

    Hwang, Alexander C; Grey, Paris H; Cuddy, Katrina; Oppenheimer, David G

    2012-01-01

    The evaluation of proteins using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis is a common technique used by biochemistry and molecular biology researchers. For laboratories that perform daily analyses of proteins, the cost of commercially available polyacrylamide gels (~$10/gel) can be considerable over time. To mitigate this cost, some researchers prepare their own polyacrylamide gels. Traditional methods of pouring these gels typically utilize specialized equipment and glass gel plates that can be expensive and preclude pouring many gels and storing them for future use. Furthermore, handling of glass plates during cleaning or gel pouring can result in accidental breakage creating a safety hazard, which may preclude their use in undergraduate laboratory classes. Our protocol demonstrates how to pour multiple protein gels simultaneously by recycling Invitrogen Nupage Novex minigel cassettes, and inexpensive materials purchased at a home improvement store. This economical and streamlined method includes a way to store the gels at 4°C for a few weeks. By re-using the plastic gel cassettes from commercially available gels, labs that run frequent protein gels can save significant costs and help the environment. In addition, plastic gel cassettes are extremely resistant to breakage, which makes them ideal for undergraduate laboratory classrooms. PMID:22349047

  18. A method for easily customizable gradient gel electrophoresis.

    PubMed

    Miller, Andrew J; Roman, Brandon; Norstrom, Eric

    2016-09-15

    Gradient polyacrylamide gel electrophoresis is a powerful tool for the resolution of polypeptides by relative mobility. Here, we present a simplified method for generating polyacrylamide gradient gels for routine analysis without the need for specialized mixing equipment. The method allows for easily customizable gradients which can be optimized for specific polypeptide resolution requirements. Moreover, the method eliminates the possibility of buffer cross contamination in mixing equipment, and the time and resources saved with this method in place of traditional gradient mixing, or the purchase of pre-cast gels, are noteworthy given the frequency with which many labs use gradient gel SDS-PAGE. PMID:27393767

  19. 2-D gel electrophoresis-based proteomic analysis reveals that ormeloxifen induces G0-G1 growth arrest and ERK-mediated apoptosis in chronic myeloid leukemia cells K562.

    PubMed

    Pal, Pooja; Kanaujiya, Jitendra K; Lochab, Savita; Tripathi, Shashi B; Bhatt, Madan L B; Singh, Pradhyumna K; Sanyal, Sabyasachi; Trivedi, Arun K

    2011-04-01

    Ormeloxifen is a nonsteroidal selective estrogen receptor modulator (SERM) and has been shown to possess anticancer activities in breast and uterine cancer. Here, we show that ormeloxifen induces apoptosis in dose-dependent manner in a variety of leukemia cells, more strikingly in K562. 2-DE-gel electrophoresis of K562 cells induced with ormeloxifen showed that 57 and 30% of proteins belong to apoptosis and cell-cycle pathways, respectively. Our data demonstrate that ormeloxifen-induced apoptosis in K562 cells involves activation of extracellular signal-regulated kinases (ERKs) and subsequent cytochrome c release, leading to mitochondria-mediated caspase-3 activation. Ormeloxifen-induced apoptosis via ERK activation was drastically inhibited by prior treatment of K562 cells with ERK inhibitor PD98059. Ormeloxifen also inhibits proliferation of K562 cells by blocking them in G0-G1 phase by inhibiting c-myc promoter via ormeloxifen-induced MBP-1 (c-myc promoter-binding protein) and upregulation of p21 expression. We further show that ormeloxifen-induced apoptosis in K562 is translatable to mononuclear cells isolated from chronic myeloid leukemia (CML) patients. Thus, ormeloxifen induces apoptosis in K562 cells via phosphorylation of ERK and arrests them in G0-G1 phase by reciprocal regulation of p21 and c-myc. Therefore, inclusion of ormeloxifen in the therapy of chronic myeloid leukemia can be of potential utility. PMID:21360677

  20. Calf-ovary protein kinases dependent on adenosine 3':5' -monophosphate. Analysis by electrophoresis and electro-focusing on polyacrylamide get.

    PubMed

    Salokangas, A; Talmadge, K; Bechtel, E; Eppenberger, U; Chrambach, A

    1977-03-01

    High resolving power and quantitative application polyacrylamide-gel electrophopresis at various pore sizes and electrofocusing provide resolution of a calf-ovarian protein-kinase system at an increased level of magnification, as well as optimal preparative routes. Three protein kinases dependent on adenosine 3':5' -monophosphate are distinguished by polyacrylamide gel electrophoresis in calf ovarian cytosol. These enzymes which are observed in the pH range 7.5--10.2, appear to be aggregates of a commonsubmit or monomer. The three kinases are, by the criteria of polyacylamide gel electrophoresis, distinct from three adenosine-3':5' -monophosphate-binding proteins found in the calf ovarian system. Analysis by electrofocusing on polyacrylamide gel shows that conventionally purified preparations of the major kinase of cytosol contain an overwhelming majority of contaminant proteins. PMID:191253

  1. Isolation, identification and characterisation of starch-interacting proteins by 2-D affinity electrophoresis.

    PubMed

    Kosar-Hashemi, Behjat; Irwin, Jennifer A; Higgins, Jody; Rahman, Sadequr; Morell, Matthew K

    2006-05-01

    A 2-D affinity electrophoretic technique (2-DAE) has been used to isolate proteins that interact with various starch components from total barley endosperm extracts. In the first dimension, proteins are separated by native PAGE. The second-dimensional gel contains polysaccharides such as amylopectin and glycogen. The migration of starch-interacting proteins in this dimension is determined by their affinity towards a particular polysaccharide and these proteins are therefore spatially separated from the bulk of proteins in the crude extract. Four distinct proteins demonstrate significant affinity for amylopectin and have been identified as starch branching enzyme I (SBEI), starch branching enzyme IIa (SBEIIa), SBEIIb and starch phosphorylase using polyclonal antibodies and zymogram activity analysis. In the case of starch phosphorylase, a protein spot was excised from a 2-DAE polyacrylamide gel and analysed using Q-TOF MS/MS, resulting in the alignment of three internal peptide sequences with the known sequence of the wheat plastidic starch phosphorylase isoform. This assignment was confirmed by the determination of the enzyme's function using zymogram analysis. Dissociation constants (Kd) were calculated for the three enzymes at 4 degrees C and values of 0.20, 0.21 and 1.3 g/L were determined for SBEI, SBEIIa and starch phosphorylase, respectively. Starch synthase I could also be resolved from the other proteins in the presence of glycogen and its identity was confirmed using a polyclonal antibody and by activity analysis. The 2-DAE method described here is simple, though powerful, enabling protein separation from crude extracts on the basis of function. PMID:16645949

  2. Consensus brain-derived protein, extraction protocol for the study of human and murine brain proteome using both 2D-DIGE and mini 2DE immunoblotting.

    PubMed

    Fernandez-Gomez, Francisco-Jose; Jumeau, Fanny; Derisbourg, Maxime; Burnouf, Sylvie; Tran, Hélène; Eddarkaoui, Sabiha; Obriot, Hélène; Dutoit-Lefevre, Virginie; Deramecourt, Vincent; Mitchell, Valérie; Lefranc, Didier; Hamdane, Malika; Blum, David; Buée, Luc; Buée-Scherrer, Valérie; Sergeant, Nicolas

    2014-01-01

    Two-dimensional gel electrophoresis (2DE) is a powerful tool to uncover proteome modifications potentially related to different physiological or pathological conditions. Basically, this technique is based on the separation of proteins according to their isoelectric point in a first step, and secondly according to their molecular weights by SDS polyacrylamide gel electrophoresis (SDS-PAGE). In this report an optimized sample preparation protocol for little amount of human post-mortem and mouse brain tissue is described. This method enables to perform both two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mini 2DE immunoblotting. The combination of these approaches allows one to not only find new proteins and/or protein modifications in their expression thanks to its compatibility with mass spectrometry detection, but also a new insight into markers validation. Thus, mini-2DE coupled to western blotting permits to identify and validate post-translational modifications, proteins catabolism and provides a qualitative comparison among different conditions and/or treatments. Herein, we provide a method to study components of protein aggregates found in AD and Lewy body dementia such as the amyloid-beta peptide and the alpha-synuclein. Our method can thus be adapted for the analysis of the proteome and insoluble proteins extract from human brain tissue and mice models too. In parallel, it may provide useful information for the study of molecular and cellular pathways involved in neurodegenerative diseases as well as potential novel biomarkers and therapeutic targets. PMID:24747743

  3. Conducting Polymer Electrodes for Gel Electrophoresis

    PubMed Central

    Bengtsson, Katarina; Nilsson, Sara; Robinson, Nathaniel D.

    2014-01-01

    In nearly all cases, electrophoresis in gels is driven via the electrolysis of water at the electrodes, where the process consumes water and produces electrochemical by-products. We have previously demonstrated that π-conjugated polymers such as poly(3,4-ethylenedioxythiophene) (PEDOT) can be placed between traditional metal electrodes and an electrolyte to mitigate electrolysis in liquid (capillary electroosmosis/electrophoresis) systems. In this report, we extend our previous result to gel electrophoresis, and show that electrodes containing PEDOT can be used with a commercial polyacrylamide gel electrophoresis system with minimal impact to the resulting gel image or the ionic transport measured during a separation. PMID:24586761

  4. Performance of 18 polymers in aluminum citrate colloidal dispersion gels

    SciTech Connect

    Smith, J.E.

    1995-11-01

    Colloidal dispersion gels are made up of low concentrations of polymer and aluminum citrate in water. These gels, which are mixed as a homogeneous solution at the surface, provide a valuable tool for in-depth blockage of high permeability regions of rock in heterogeneous reservoirs. Performance of colloidal dispersion gels depends strongly on the type and quality of polymer used. This paper provides an overview of the performance of 18 different polymers in colloidal dispersion gels. 14 of the polymers were partially hydrolyzed polyacrylamides or AMPS polymers in dry crystalline form with varying degrees of hydrolysis and molecular weight. The group also includes one cationic polyacrylamide, one carboxymethyl cellulose, one partially hydrolyzed polyacrylamide in emulsion form and one polysaccharide in dry form. Gels were mixed with the polymers at two polymer concentrations, three polymer:aluminum ratios and in different concentrations of potassium chloride. The gels were quantitatively tested at 1, 7, 14 and 28 days after crosslinking using the transition pressure test, which is a screen flow resistance test. Of the six polymer types tested, only the dry partially hydrolyzed polyacrylamides and AMPS polymers formed colloidal dispersion gels. Gel strength generally increased with increasing anionic charge and molecular weight; however, the manner in which the polymer is manufactured and the impurities present in the polymer also play roles which are more significant than originally expected.

  5. Substituted Imidazole of 5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine Inactivates Cytochrome P450 2D6 by Protein Adduction

    PubMed Central

    Nagy, Leslie D.; Mocny, Catherine S.; Diffenderfer, Laura E.; Hsi, David J.; Butler, Brendan F.; Arthur, Evan J.; Fletke, Kyle J.; Palamanda, Jairam R.; Nomeir, Amin A.

    2011-01-01

    5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine (SCH 66712) is a potent mechanism-based inactivator of human cytochrome P450 2D6 that displays type I binding spectra with a Ks of 0.39 ± 0.10 μM. The partition ratio is ∼3, indicating potent inactivation that addition of exogenous nucleophiles does not prevent. Within 15 min of incubation with SCH 66712 and NADPH, ∼90% of CYP2D6 activity is lost with only ∼20% loss in ability to bind CO and ∼25% loss of native heme over the same time. The stoichiometry of binding to the protein was 1.2:1. SDS-polyacrylamide gel electrophoresis with Western blotting and autoradiography analyses of CYP2D6 after incubations with radiolabeled SCH 66712 further support the presence of a protein adduct. Metabolites of SCH 66712 detected by mass spectrometry indicate that the phenyl group on the imidazole ring of SCH 66712 is one site of oxidation by CYP2D6 and could lead to methylene quinone formation. Three other metabolites were also observed. For understanding the metabolic pathway that leads to CYP2D6 inactivation, metabolism studies with CYP2C9 and CYP2C19 were performed because neither of these enzymes is significantly inhibited by SCH 66712. The metabolites formed by CYP2C9 and CYP2C19 are the same as those seen with CYP2D6, although in different abundance. Modeling studies with CYP2D6 revealed potential roles of various active site residues in the oxidation of SCH 66712 and inactivation of CYP2D6 and showed that the phenyl group of SCH 66712 is positioned at 2.2 Å from the heme iron. PMID:21422192

  6. High divergent 2D grating

    NASA Astrophysics Data System (ADS)

    Wang, Jin; Ma, Jianyong; Zhou, Changhe

    2014-11-01

    A 3×3 high divergent 2D-grating with period of 3.842μm at wavelength of 850nm under normal incidence is designed and fabricated in this paper. This high divergent 2D-grating is designed by the vector theory. The Rigorous Coupled Wave Analysis (RCWA) in association with the simulated annealing (SA) is adopted to calculate and optimize this 2D-grating.The properties of this grating are also investigated by the RCWA. The diffraction angles are more than 10 degrees in the whole wavelength band, which are bigger than the traditional 2D-grating. In addition, the small period of grating increases the difficulties of fabrication. So we fabricate the 2D-gratings by direct laser writing (DLW) instead of traditional manufacturing method. Then the method of ICP etching is used to obtain the high divergent 2D-grating.

  7. Polyacrylamide Hydrogel Properties for Horticultural Applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Polyacrylamide (PAAm) hydrogels are commonly employed to ensure hydration of the growth media and minimize crop losses during the crop production and postproduction phases in horticulture. However, studies of the effect of these materials have shown that they have a minimal effect on crop life and q...

  8. N-terminal specific conjugation of extracellular matrix proteins to 2-pyridinecarboxaldehyde functionalized polyacrylamide hydrogels.

    PubMed

    Lee, Jessica P; Kassianidou, Elena; MacDonald, James I; Francis, Matthew B; Kumar, Sanjay

    2016-09-01

    Polyacrylamide hydrogels have been used extensively to study cell responses to the mechanical and biochemical properties of extracellular matrix substrates. A key step in fabricating these substrates is the conjugation of cell adhesion proteins to the polyacrylamide surfaces, which typically involves nonspecifically anchoring these proteins via side-chain functional groups. This can result in a loss of presentation control and altered bioactivity. Here, we describe a new functionalization strategy in which we anchor full-length extracellular matrix proteins to polyacrylamide substrates using 2-pyridinecarboxaldehyde, which can be co-polymerized into polyacrylamide gels and used to immobilize proteins by their N-termini. This one-step reaction proceeds under mild aqueous conditions and does not require additional reagents. We demonstrate that these substrates can readily conjugate to various extracellular matrix proteins, as well as promote cell adhesion and spreading. Notably, this chemistry supports the assembly and cellular remodeling of large collagen fibers, which is not observed using conventional side-chain amine-conjugation chemistry. PMID:27348850

  9. 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

  10. Microfabricated Polyacrylamide Devices for the Controlled Culture of Growing Cells and Developing Organisms

    PubMed Central

    Gude, Sebastian; Recouvreux, Pierre; van Zon, Jeroen S.; Tans, Sander J.

    2013-01-01

    The ability to spatially confine living cells or small organisms while dynamically controlling their aqueous environment is important for a host of microscopy applications. Here, we show how polyacrylamide layers can be patterned to construct simple microfluidic devices for this purpose. We find that polyacrylamide gels can be molded like PDMS into micron-scale structures that can enclose organisms, while being permeable to liquids, and transparent to allow for microscopic observation. We present a range of chemostat-like devices to observe bacterial and yeast growth, and C. elegans nematode development. The devices can integrate PDMS layers and allow for temporal control of nutrient conditions and the presence of drugs on a minute timescale. We show how spatial confinement of motile C. elegans enables for time-lapse microscopy in a parallel fashion. PMID:24086559

  11. Porosity-Tuned Chitosan-Polyacrylamide Hydrogel Microspheres for Improved Protein Conjugation.

    PubMed

    Jung, Sukwon; Abel, John H; Starger, Jesse L; Yi, Hyunmin

    2016-07-11

    We report a robust method to manufacture polyacrylamide-based functional hydrogel microspheres with readily tunable macroporous structures by utilizing a simple micromolding-based technique. Specifically, surface tension-induced droplet formation of aqueous solutions of chitosan and acrylamide in 2D-shaped micromolds followed by photoinduced polymerization leads to monodisperse microspheres. Pore sizes of the microspheres can be readily tuned by simple addition of inert long-chain poly(ethylene glycol) porogen at low content in the prepolymer solution. The as-prepared chitosan-polyacrylamide microspheres exhibit chemical functionality through chitosan's primary amines, rapid protein conjugation with selective tetrazine-trans-cyclooctene reaction, and nonfouling property. Combined with the potential to create anisotropic network structures, we envision that our simple fabrication-conjugation method would offer a potent route to manufacture a variety of biofunctionalized hydrogel microentities. PMID:27351270

  12. Monitoring the gelation of polyacrylamide-sodium alginate composite by fluorescence technique

    NASA Astrophysics Data System (ADS)

    Akın Evingür, Gülşen; Tezcan, Filiz; Bedia Erim, F.; Pekcan, Önder

    2012-06-01

    Polyacrylamide (PAAm)-sodium alginate (SA) composite was prepared with different amounts of SA varying in the range between 0.06% and 2% (w/v). The PAAm-SA composite was characterized by the steady-state fluorescence technique. Pyranine was added as a fluoroprobe for monitoring the polymerization. It was observed that pyranine molecules bind to AAm and SA chains upon the initiation of the polymerization. Thus, the fluorescence spectra of the bonded pyranines shift to the shorter wavelengths. Fluorescence spectra from the bonded pyranines allowed us to monitor the sol-gel phase transition, and to test the universality of the sol-gel transition as a function of SA contents. Observations around the critical point show that the gel fraction exponent, β, and the weight average degree of polymerization exponent, γ, agreed with the percolation result for (<0.25% (w/v)) SA contents. However, classical results were produced at (<2% (w/v)) SA contents.

  13. 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.

  14. AnisWave 2D

    2004-08-01

    AnisWave2D is a 2D finite-difference code for a simulating seismic wave propagation in fully anisotropic materials. The code is implemented to run in parallel over multiple processors and is fully portable. A mesh refinement algorithm has been utilized to allow the grid-spacing to be tailored to the velocity model, avoiding the over-sampling of high-velocity materials that usually occurs in fixed-grid schemes.

  15. Reproducibility of an Integrated Quantitation Method Coupling 2D GeLC-MS/MS with the emPAI for Comparative Proteomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2D gel mapping, most protein spots consist of multiple proteins posing a significant challenge for the proper interpretation of gel-based comparative experiments. Previously we introduced an approach integrating 2-D difference gel electrophoresis and LC-MS/MS analysis with the exponentially modif...

  16. A simple and cost-effective solid-phase protein nano-assay using polyacrylamide-coated glass plates.

    PubMed

    Krajewski, Wladyslaw A

    2015-02-01

    A new solid-phase protein nano-assay is suggested for simple and sensitive estimation of protein content in sample buffers (a 1-μl sample is sufficient for analysis). The assay is different from conventional "on-filter" assays in that it uses inexpensive fully transparent polyacrylamide gel (PAAG)-coated glass plates as solid support and, thus, combines the convenience of "on-membrane" staining with the sensitivity and ease of documentation of "in-gel" staining (and, therefore, is especially suited for standard lab gel documentation systems). The PAAG plates assay is compatible with all dyes for in-gel protein staining. Depending on the sensitivity of the staining protocol, the assay can be used in macro-, micro-, and nano-assay formats. We also describe a low-cost two-component colloidal Coomassie brilliant blue G-250 (CBB G-250) staining protocol for fast quantitative visualization of proteins spotted on a PAAG plate (the detection limit is up to 2 ng of proteins even when using a Nikon CoolPix digital camera and white light transilluminator instead of a gel scanner). The suggested colloidal CBB G-250 protocol could also be used for visualizing nano-amounts of proteins in polyacrylamide gels. The PAAG plate assay could be useful for proteomic applications and, in general, for all cases where a fast, sensitive, and easily documentable cost-effective solid-phase protein assay is required. PMID:25449300

  17. Radio-synthesized polyacrylamide hydrogels for proteins release

    NASA Astrophysics Data System (ADS)

    Ferraz, Caroline C.; Varca, Gustavo H. C.; Lopes, Patricia S.; Mathor, Monica B.; Lugão, Ademar B.

    2014-01-01

    The use of hydrogels for biomedical purposes has been extensively investigated. Pharmaceutical proteins correspond to highly active substances which may be applied for distinct purposes. This work concerns the development of radio-synthesized hydrogel for protein release, using papain and bovine serum albumin as model proteins. The polymer was solubilized (1% w/v) in water and lyophilized. The proteins were incorporated into the lyophilized polymer and the hydrogels were produced by simultaneous crosslinking and sterilization using γ-radiation under frozen conditions. The produced systems were characterized in terms of swelling degree, gel fraction, crosslinking density and evaluated according to protein release, bioactivity and cytotoxicity. The hydrogels developed presented different properties as a function of polymer concentration and the optimized results were found for the samples containing 4-5% (w/v) polyacrylamide. Protein release was controlled by the electrostatic affinity of acrylic moieties and proteins. This selection was based on the release of the proteins during the experiment period (up to 50 h), maintenance of enzyme activity and the nanostructure developed. The system was suitable for protein loading and release and according to the cytotoxic assay it was also adequate for biomedical purposes, however this method was not able to generate a matrix with controlled pore sizes.

  18. Large unilateral breast autoinflation after breastfeeding linked to polyacrylamide hydrogel injection augmentation mammaplasty.

    PubMed

    Kang, Gavin Chun-Wui; Ong, Yee Siang

    2011-02-01

    Augmentation mammaplasty using polyacrylamide hydrogel (PAAG) injection is associated with myriad complications. A patient treated by the authors had bilateral breast augmentation with PAAG injection and experienced large unilateral right breast autoinflation after breastfeeding, which required surgical clearance of a likely galactocele or sterile pus collection that resulted in deformity. Patients with PAAG filler injection-augmented breasts should avoid breastfeeding. The authors recommend against using PAAG injection for augmentation mammaplasty, especially in women intending to breastfeed. Physicians and patients must be aware of the complications associated with PAAG before gel administration. PMID:20652566

  19. Breast cancer following polyacrylamide hydrogel injection for breast augmentation: A case report

    PubMed Central

    CHEN, GANG; WANG, YUJIA; HUANG, JIN-LONG

    2016-01-01

    Polyacrylamide hydrogel (PAAG) has been used for several years as an injectable implant for augmentation mammoplasty in China. Although patients who received PAAG injections experienced a number of complications, breast cancer following PAAG injection has been reported only in two cases. In this report, we present a case of breast cancer following PAAG injection for breast augmentation. Our study demonstrated that PAAG injection may increase the risk of breast cancer development. Early-stage breast cancer detection is difficult, since the breast is covered with the indurated injected gel. Thus, PAAG injection for augmentation mammoplasty may negatively affect breast cancer diagnosis and prognosis. PMID:26998299

  20. Data of microstructure and mechanical properties of carbon foams derived from sucrose/polyacrylamide hydrogel

    PubMed Central

    Yao, Yao; Chen, Fei; Chen, Xi; Shen, Qiang; Zhang, Lianmeng

    2016-01-01

    An easy method that combined gel casting and physical foaming was used to fabricate modified carbon foams. The design of carbon foams from sucrose/polyacrylamide hydrogel is a new concept for controlling the microstructure and improving the compressive properties of carbon foams. This article provides the micrographs obtained from optical and scanning electron microscope for foaming solution and carbon foams. Weight loss data used to construct the thermo-gravimetric curves are included. Load–displacement data constructing the stress–strain curves and the derived compressive properties are also included. PMID:26933668

  1. Data of microstructure and mechanical properties of carbon foams derived from sucrose/polyacrylamide hydrogel.

    PubMed

    Yao, Yao; Chen, Fei; Chen, Xi; Shen, Qiang; Zhang, Lianmeng

    2016-06-01

    An easy method that combined gel casting and physical foaming was used to fabricate modified carbon foams. The design of carbon foams from sucrose/polyacrylamide hydrogel is a new concept for controlling the microstructure and improving the compressive properties of carbon foams. This article provides the micrographs obtained from optical and scanning electron microscope for foaming solution and carbon foams. Weight loss data used to construct the thermo-gravimetric curves are included. Load-displacement data constructing the stress-strain curves and the derived compressive properties are also included. PMID:26933668

  2. Photoswitchable gel assembly based on molecular recognition.

    PubMed

    Yamaguchi, Hiroyasu; Kobayashi, Yuichiro; Kobayashi, Ryosuke; Takashima, Yoshinori; Hashidzume, Akihito; Harada, Akira

    2012-01-01

    The formation of effective and precise linkages in bottom-up or top-down processes is important for the development of self-assembled materials. Self-assembly through molecular recognition events is a powerful tool for producing functionalized materials. Photoresponsive molecular recognition systems can permit the creation of photoregulated self-assembled macroscopic objects. Here we demonstrate that macroscopic gel assembly can be highly regulated through photoisomerization of an azobenzene moiety that interacts differently with two host molecules. A photoregulated gel assembly system is developed using polyacrylamide-based hydrogels functionalized with azobenzene (guest) or cyclodextrin (host) moieties. Reversible adhesion and dissociation of the host gel from the guest gel may be controlled by photoirradiation. The differential affinities of α-cyclodextrin or β-cyclodextrin for the trans-azobenzene and cis-azobenzene are employed in the construction of a photoswitchable gel assembly system. PMID:22215078

  3. Photoswitchable gel assembly based on molecular recognition

    PubMed Central

    Yamaguchi, Hiroyasu; Kobayashi, Yuichiro; Kobayashi, Ryosuke; Takashima, Yoshinori; Hashidzume, Akihito; Harada, Akira

    2012-01-01

    The formation of effective and precise linkages in bottom-up or top-down processes is important for the development of self-assembled materials. Self-assembly through molecular recognition events is a powerful tool for producing functionalized materials. Photoresponsive molecular recognition systems can permit the creation of photoregulated self-assembled macroscopic objects. Here we demonstrate that macroscopic gel assembly can be highly regulated through photoisomerization of an azobenzene moiety that interacts differently with two host molecules. A photoregulated gel assembly system is developed using polyacrylamide-based hydrogels functionalized with azobenzene (guest) or cyclodextrin (host) moieties. Reversible adhesion and dissociation of the host gel from the guest gel may be controlled by photoirradiation. The differential affinities of α-cyclodextrin or β-cyclodextrin for the trans-azobenzene and cis-azobenzene are employed in the construction of a photoswitchable gel assembly system. PMID:22215078

  4. Improving immobilized biocatalysts by gel phase polymerization

    SciTech Connect

    Kuu, W.Y.; Polack, J.A.

    1983-08-01

    A new method is presented for the treatment of gel-type supports, used for immobilizing microbial cells and enzymes, to obtain high mechanical strength. It is particularly useful for ethanol fermentation over gel beads containing immobilized viable cells, where the beads can be ruptured by gas production and the growth of cells within the gels. This method consists of treating agar or carrageenan gel with polyacrylamide to form a rigid support which retains the high catalytic activity characteristic of the untreated biocatalysts. The size and shape of the biocatalyst is unaffected by this treatment. The method involves the diffusion of acrylamide, N,N'-methylenebisacrylamide and BETA-dimethylaminopropionitrile (or N,N,N',N'-tetramethylethylenediamine) into the preformed biocatalyst beads followed by the addition of an initiator to cause polymerization within the beads. Treated gels have been used for the continuous fermentation of glucose to ethanol in a packed column for over two months.

  5. Transverse agarose pore gradient gel electrophoresis of DNA.

    PubMed

    Fawcett, J S; Wheeler, D; Chrambach, A

    1992-06-01

    Transverse agarose pore gradient gels were prepared on GelBond in the concentration range of nominally 0.2-1.5% SeaKem GTG agarose, using density stabilization by glycerol and incorporation of a dye to define the gel concentration at each point on the pore gradient gel. The distribution of the dye was evaluated by photography, video-acquisition and digitization of the gradient mixture and by densitometry of the gel. The gel was applied to the electrophoresis of a 1-kb standard ladder of DNA fragments, using standard submarine apparatus. The method extends to agarose gel electrophoresis the benefits of semi-automated analysis of 'Ferguson curves' described in application to polyacrylamide gel by Wheeler et al. (J. Biochem. Biophys. Methods 24, 171-180). PMID:1640052

  6. Stacking up 2D materials

    NASA Astrophysics Data System (ADS)

    Mayor, Louise

    2016-05-01

    Graphene might be the most famous example, but there are other 2D materials and compounds too. Louise Mayor explains how these atomically thin sheets can be layered together to create flexible “van der Waals heterostructures”, which could lead to a range of novel applications.

  7. Molecular recognition in gels, monolayers, and solids

    NASA Astrophysics Data System (ADS)

    Prime, Kevin L.; Chu, Yen-Ho; Schmid, Walther; Seto, Christopher T.; Chen, James K.

    1991-12-01

    This paper describes work in four areas: affinity electrophoresis of carbonic anhydrase in cross-linked polyacrylamide derived gels containing immobilized derivatives of aryl sulfonamides; inhibition of the hemagglutination of erythrocytes induced by influenza virus using water-soluble polyacrylamides bearing sialic acid groups; the application of self-assembled monolayers (SAMs) of alkyl thiolates on gold to the study of protein adsorption on organic surfaces; and the use of networks of hydrogen bonds to generate new classes of non-covalently assembled organic materials, both in solution and in crystals. This paper summarizes research in two areas of molecular recognition: affinity polymers and molecular self assembly. We illustrate these areas by examples drawn from affinity gel electrophoresis, soluble synthetic macromolecular inhibitors of binding of influenza virus to erythrocytes protein adsorption on self assembled monolayers and self assembling hydrogen bonded molecular aggregates.

  8. MOSS2D V1

    2001-01-31

    This software reduces the data from two-dimensional kSA MOS program, k-Space Associates, Ann Arbor, MI. Initial MOS data is recorded without headers in 38 columns, with one row of data per acquisition per lase beam tracked. The final MOSS 2d data file is reduced, graphed, and saved in a tab-delimited column format with headers that can be plotted in any graphing software.

  9. Influence of gel dimensions on resolution and sample throughput on two-dimensional gels.

    PubMed

    Lee, KiBeom; Pi, KyungBae; Lee, Hong-Gu

    2008-04-01

    To achieve high throughput and economical format of 2-D PAGE, comparison between gel size and resolution was conducted on human breast carcinoma cell line (MCF-7/AZ) proteins. SDS gel length showed a weaker influence of separation length on resolution in the second dimension, and there was little benefit of separation distances greater than 15 to 19 cm. IPG strip separation distances were very important with dramatic increase in resolution of longer gels compared with smaller gels, and maximal resolution was obtained using 18- and 24-cm IPG strips. Loading optimal amount of proteins on 2-D gels can also increase the number of detected spots. Therefore, taken together, compromise 2-D gels are crucial for higher capacity and higher throughput. PMID:18457572

  10. Gel placement in fractured systems

    SciTech Connect

    Seright, R.S.

    1995-11-01

    This paper examines several factors that can have an important effect on gel placement in fractured systems, including gelant viscosity, degree of gelation, and gravity. For an effective gel treatment, the conductivity of the fracture must be reduced and a viable flow path must remain open between the wellbore and mobile oil in the reservoir. During placement, the gelant that``leaks off`` from the fracture into the rock plays an important role in determining how well a gel treatment will reduce channeling. For a given volume of gelant injected the distance of gelant leakoff is greater for a viscous gelant than for a low-viscosity gelant. In one method to minimize gelant leakoff, sufficient gelation is designed to occur before the gelant leaves the wellbore. The authors investigated this approach in numerous experiments with both fractured and unfractured cores. They studied Cr(III)/acetate/hydrolyzed polyacrylamide (HPAM), resorcinol/formaldehyde, Cr(III)/xanthan, aluminum/citrate/HPAM, and other gelants and gels with various delay times between gelant preparation and injection. Their results suggest both hope and caution concerning the injection of gels into fractured systems.

  11. Microscale 2D separation systems for proteomic analysis

    PubMed Central

    Xu, Xin; Liu, Ke; Fan, Z. Hugh

    2012-01-01

    Microscale 2D separation systems have been implemented in capillaries and microfabricated channels. They offer advantages of faster analysis, higher separation efficiency and less sample consumption than the conventional methods, such as liquid chromatography (LC) in a column and slab gel electrophoresis. In this article, we review their recent advancement, focusing on three types of platforms, including 2D capillary electrophoresis (CE), CE coupling with capillary LC, and microfluidic devices. A variety of CE and LC modes have been employed to construct 2D separation systems via sophistically designed interfaces. Coupling of different separation modes has also been realized in a number of microfluidic devices. These separation systems have been applied for the proteomic analysis of various biological samples, ranging from a single cell to tumor tissues. PMID:22462786

  12. 21 CFR 173.10 - Modified polyacrylamide resin.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... CONSUMPTION Polymer Substances and Polymer Adjuvants for Food Treatment § 173.10 Modified polyacrylamide resin... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Modified polyacrylamide resin. 173.10 Section 173.10 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES...

  13. 21 CFR 173.10 - Modified polyacrylamide resin.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... CONSUMPTION Polymer Substances and Polymer Adjuvants for Food Treatment § 173.10 Modified polyacrylamide resin... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Modified polyacrylamide resin. 173.10 Section 173.10 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES...

  14. [In situ photopolymerization of polyacrylamide-based preconcentrator on a microfluidic chip for capillary electrophoresis].

    PubMed

    Yamamoto, Sachio

    2012-01-01

    Microchip electrophoresis is widely used for microfluidics and has been studied extensively over the past decade. Translation of capillary electrophoresis methods from traditional capillary systems to a microchip platform provides rapid separation and easy quantitation of sample components. However, most microfluidic systems suffer from critical scaling problems. One promising solution to this problem is online sample preconcentration of all analytes in a sample reservoir before the separation channel. Herein, the following three techniques for online preconcentration during microchip electrophoresis are proposed: (1) in situ fabrication of an ionic polyacrylamide-based preconcentrator on a simple poly(methyl methacrylate) microfluidic chip for perm-selective preconcentration and capillary electrophoretic separation of anionic compounds, (2) simultaneous concentration enrichment and electrophoretic separation of weak acids on a microchip using an in situ photopolymerized carboxylate-type polyacrylamide gels as the perm-selective preconcentrator, and (3) microchip electrophoresis of oligosaccharides using lectin-immobilized preconcentrator gels fabricated by in situ photopolymerization. These techniques are expected to be powerful tools for clinical and pharmaceutical studies with on-line preconcentration during microchip electrophoresis. PMID:23023420

  15. Characterization of polyacrylamide based monolithic columns.

    PubMed

    Plieva, Fatima M; Andersson, Jonatan; Galaev, Igor Yu; Mattiasson, Bo

    2004-07-01

    Supermacroporous monolithic polyacrylamide (pAAm)-based columns have been prepared by radical cryo-copolymerization (copolymerization in the moderately frozen system) of acrylamide with functional co-monomer, allyl glycidyl ether (AGE), and cross-linker N,N'-methylene-bis-acrylamide (MBAAm) directly in glass columns (ID 10 mm). The monolithic columns have uniform supermacroporous sponge-like structure with interconnected supermacropores of pore size 5-100 microm. The monoliths can be dried and stored in the dry state. High mechanical stability of the monoliths allowed sterilization by autoclaving. Column-to-column reproducibility of pAAm-monoliths was demonstrated on 5 monolithic columns from different batches prepared under the same cryostructuration conditions. PMID:15354560

  16. Nanoimprint lithography: 2D or not 2D? A review

    NASA Astrophysics Data System (ADS)

    Schift, Helmut

    2015-11-01

    Nanoimprint lithography (NIL) is more than a planar high-end technology for the patterning of wafer-like substrates. It is essentially a 3D process, because it replicates various stamp topographies by 3D displacement of material and takes advantage of the bending of stamps while the mold cavities are filled. But at the same time, it keeps all assets of a 2D technique being able to pattern thin masking layers like in photon- and electron-based traditional lithography. This review reports about 20 years of development of replication techniques at Paul Scherrer Institut, with a focus on 3D aspects of molding, which enable NIL to stay 2D, but at the same time enable 3D applications which are "more than Moore." As an example, the manufacturing of a demonstrator for backlighting applications based on thermally activated selective topography equilibration will be presented. This technique allows generating almost arbitrary sloped, convex and concave profiles in the same polymer film with dimensions in micro- and nanometer scale.

  17. 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...

  18. 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...

  19. 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...

  20. 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.

  1. 2D dose distribution images of a hybrid low field MRI-γ detector

    NASA Astrophysics Data System (ADS)

    Abril, A.; Agulles-Pedrós, L.

    2016-07-01

    The proposed hybrid system is a combination of a low field MRI and dosimetric gel as a γ detector. The readout system is based on the polymerization process induced by the gel radiation. A gel dose map is obtained which represents the functional part of hybrid image alongside with the anatomical MRI one. Both images should be taken while the patient with a radiopharmaceutical is located inside the MRI system with a gel detector matrix. A relevant aspect of this proposal is that the dosimetric gel has never been used to acquire medical images. The results presented show the interaction of the 99mTc source with the dosimetric gel simulated in Geant4. The purpose was to obtain the planar γ 2D-image. The different source configurations are studied to explore the ability of the gel as radiation detector through the following parameters; resolution, shape definition and radio-pharmaceutical concentration.

  2. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods

    PubMed Central

    Gauci, Victoria J.; Wright, Elise P.

    2010-01-01

    Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist. PMID:21686332

  3. Polyelectrolyte gels

    SciTech Connect

    Segalman, D.J.; Witkowski, W.R.

    1995-06-01

    Polyelectrolyte (PE) gels are swollen polymer/solvent networks that undergo a reversible volume collapse/expansion through various types of stimulation. Applications that could exploit this large deformation and solvent expulsion/absorption characteristics include robotic {open_quotes}fingers{close_quotes} and drug delivery systems. The goals of the research were to first explore the feasibility of using the PE gels as {open_quotes}smart materials{close_quotes} - materials whose response can be controlled by an external stimulus through a feedback mechanism. Then develop a predictive capability to simulate the dynamic behavior of these gels. This involved experimentally characterizing the response of well-characterized gels to an applied electric field and other stimuli to develop an understanding of the underlying mechanisms which cause the volume collapse. Lastly, the numerical analysis tool was used to simulate various potential engineering devices based on PE gels. This report discusses the pursuit of those goals through experimental and computational means.

  4. Microbial degradation of polyacrylamide by aerobic granules.

    PubMed

    Liu, Lili; Wang, Zhiping; Lin, Kuangfei; Cai, Weimin

    2012-01-01

    To deal with polyacrylamide (PAM) wastewater, granular sludge formed in glucose-fed sequencing batch reactors (SBR) was employed to cultivate PAM-degrading granules. Three replicated SBRs were operated with increasing PAM concentration in the influent from 67 to 670 mg L(-1), and the hydraulic retention time was increased at the same time from 1 d to 6 d during the six-phase of the 43 d acclimation period. The well-acclimated PAM-degrading granules were different from the seeding granules in colour, mean diameter, biomass density and settle ability, and could use PAM as the sole carbon and nitrogen source. In the batch experiments, PAM degradation rate by granules was determined as 2.23 mg PAM g(-1) MLSS h(-1). According to the analysis of the intermediates of PAM biodegradation, PAM was degraded initially through hydrolysis of the amide group, and no acrylamide monomer was detected. With the help of LC/MS, the main intermediate was identified as polyacrylic acid with a low molecular weight. Therefore, the PAM-degrading granular sludge may be employed for removing PAM in the wastewater produced from tertiary oil recovery that uses polymeric flooding technology. PMID:22720433

  5. Field demonstration of in situ grouting of radioactive solid waste burial trenches with polyacrylamide. [Polyacrylamide

    SciTech Connect

    Spalding, B.P.; Fontaine, T.A.

    1990-01-01

    Demonstrations of in situ grouting with polyacrylamide were carried out on two undisturbed burial trenches and one dynamically compacted burial trench in Solid Waste Storage Area (SWSA) 6 at Oak Ridge National Laboratory (ORNL). The injection of polyacrylamide was achieved quite facilely for the two undisturbed burial trenches which were filled with grout, at typical pumping rates of 95 L/min, in several batches injected over several days. The compacted burial trench, however, failed to accept grout at more than 1.9 L/min even when pressure was applied. Thus, it appears that burial trenches, stabilized by dynamic compaction, have a permeability too low to be considered groutable. The water table beneath the burial trenches did not respond to grout injections indicating a lack of hydrologic connection between fluid grout and the water table which would have been observed if the grout failed to set. Because grout set times were adjusted to less than 60 min, the lack of hydrologic connection was not surprising. Postgrouting penetration testing revealed that the stability of the burial trenches was increased from 26% to 79% that measured in the undisturbed soil surrounding the trenches. In situ permeation tests on the grouted trenches indicated a significant reduction in hydraulic conductivity of the trench contents from a mean of 2.1 {times} 10{sup {minus}3} to 1.85 {times} 10{sup {minus}5} cm/s. Preliminary observations indicated that grouting with polyacrylamide is an excellent method for both improved stability and hydrologic isolation of radioactive waste and its incidental hazardous constituents.

  6. In situ grouting of buried transuranic waste with polyacrylamide

    SciTech Connect

    Spalding, B.P.; Lee, S.Y.; Farmer, C.D.; Hyder, L.K.; Supaokit, P.

    1987-01-01

    This project is a demonstration and evaluation of the in situ hydrologic stabilization of buried transuranic waste at a humid site via grout injection. Two small trenches, containing buried transuranic waste, were filled with 34.000 L of polyacrylamide grout. Initial field results have indicated that voids within the trenches were totally filled by the grout and that the intratrench hydraulic conductivity was reduced to below field-measurable values. No evidence of grout constituents were observed in twelve perimeter groundwater monitoring wells indicating that grout was contained completely within the two trenches. Polyacrylamide grout was selected for field demonstration over the polyacrylate grout due to its superior performance in laboratory degradation studies. Also supporting the selection of polyacrylamide was the difficulty in controlling the set time of the acrylate polymerization. Based on preliminary degradation monitoring, the polyacrylamide was estimated to have a microbiological half-life of 362 years in the test soil. 15 refs., 9 figs., 12 tabs.

  7. Improving gel properties of hairtail surimi by electron irradiation

    NASA Astrophysics Data System (ADS)

    Lin, Xianping; Yang, Wenge; Xu, Dalun; Jie, Zhen; Liu, Wen

    2015-05-01

    Hairtail surimi was subjected to electron irradiation for doses up to 9 kGy. At 7 kGy highest gel strength was achieved. The irradiation also increased lightness and expressible water amount. Scanning electron micrographs showed that 7 kGy irradiation made the surimi protein gel network more compact. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) revealed the degradation of myosin heavy chain (MHC) as the irradiation dose increased, particularly at the 7 and 9 kGy doses. Radiation processing may become a new effective tool in surimi production.

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

    SciTech Connect

    Campbell, Warren G.; Jirasek, Andrew; 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. 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. 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

  9. Electrochemical stimulation and control of electroactive polymer gels

    NASA Astrophysics Data System (ADS)

    Guelch, Rainer W.; Holdenried, Jens; Weible, Andrea; Wallmersperger, Thomas; Kroeplin, Bernd

    2001-07-01

    Direct effects of electrical currents on polyelectrolyte gels are always associated with changes in their Donnan potential. Thus electrical stimulation of gels can be only completely understood if the direct effect of electric fields on the potential profile within the gels are known. The purpose of this study is to present recordings of Donnan potentials in electroactive gels of various compositions, especially under the influence of electric fields. An important finding is that opposite alterations in the Donnan potential simultaneously occur at the current inflow and outflow region of the gel. In anionic gels hyperpolarization, i.e. higher negativity, is induced on the anode-side of the gel, whereas depolarization is found on the cathode-side. As these shifts in the potential are supposed to affect swelling or deswelling of polyelectrolyte gels, they will primarily promote bending motions of the gel. To demonstrate the opposite bending behavior of anionic and cationic polymer gels under the influence of an electric field a short video sequence of an EAP gripper in action is presented. It is made exclusively of polyelectrolyte gel strips taking advantage of the fact that anionic and cationic polyacrylamide gels can be attached firmly to each other without any adhesive.

  10. Improving immobilized biocatalysts by gel phase polymerization

    SciTech Connect

    Kuu, W.Y.; Polack, J.A.

    1983-08-01

    A new method is presented for the treatment of gel-type supports, used for immobilizing microbial cells and enzymes, to obtain high mechanical strength. It is particularly useful for ethanol fermentation over gel beads containing immobilized viable cells, where the beads can be ruptured by gas production and the growth of cells within the gels. This method consists of treating agar or carrageenan gel with polyacrylamide to form a rigid support which retains the high catalytic activity characteristic of the untreated biocatalysts. The size and shape of the biocatalyst is unaffected by this treatment. The method involves the diffusion of acrylamide, N,N'-methylenebisacrylamide and ..beta..-dimethylaminopropionitrile (or N,N,N',N'-tetramethylethylenediamine) into the preformed biocatalyst beads followed by the addition of an initiator to cause polymerization within the beads. Treated gels have been used for the continuous fermentation of glucose to ethanol in a packed column for over two months. During this operation, the gel beads maintained their rigidity, and the maximum productivity was as high as 50 gh/sup -1/ L/sup -1/ gel. There was no appreciable decay of cell activity.

  11. DNA sequencing by capillary electrophoresis with replaceable linear polyacrylamide and laser-induced fluorescence detection.

    PubMed

    Ruiz-Martinez, M C; Berka, J; Belenkii, A; Foret, F; Miller, A W; Karger, B L

    1993-10-15

    Replaceable linear polyacrylamide (LPA) has been utilized as a sieving matrix for DNA sequencing by capillary electrophoresis (CE). Difficulties associated with cross-linked polyacrylamide gel stability have been overcome for the routine application of CE to DNA sequencing. A simple laser-induced fluorescence (LIF) detection system based on a single laser and two photomultipliers (PMT) has been adopted for this work. Sequencing information for four bases has been obtained from two fluorescent dyes and two peak height ratios, detected in two optical channels. FAM- and JOE-labeled M13 (-21) primers have been chosen because both dyes are efficiently excited with a low-power argon ion laser, can be optically separated, and exhibit minimal dye-based shifts in DNA fragment mobilities. Addition of denaturants to the electrophoresis running buffer (1 x TBE, 3.5 M urea, 30% formamide) and column operation at 32 degrees C permitted the resolution of difficult compressed sites in the sequence of phage M13mp18. Careful examination of the polymerization reaction of LPA has led to methodology that has proven to be reproducible for obtaining DNA sequencing information of M13mp18 phage for 350 nucleotides in close to 30 min. PMID:8250265

  12. Effect of gel structure of matrix orientation in pulsed alternating electric fields

    SciTech Connect

    Stellwagen, N.C.; Stellwagen, J.

    1993-12-31

    Four polymeric gels with different structures, LE agarose, HEEO agarose, beta-carrageenan, and polyacrylamide, were studied by transient electric birefringence to determine the importance of various structural features on the orientation of the gels in pulsed alternating electric fields. The birefrigence relaxation times observed for agarose gels in low voltage electric fields suggest that long fibers and/or domains, ranging up to tens of microns in size, are oriented by the electric field. The sign of the birefringence reverses when the direction of the electric field is reversed, suggesting that the oriented domains change their direction of orientation from parallel to perpendicular (or vice versa) when the polarity of the electric field is reversed. These anamalous orientation effects are observed with both types of agarose gels, but not with beta-carrageenan or polyacrylamide gels, suggesting that the alternating D,L galactose residues in the agarose backbone are responsible for the anomalies.

  13. Tissue integration of polyacrylamide hydrogel: an experimental study of periurethral, perivesical, and mammary gland tissue in the pig.

    PubMed

    Christensen, Lise H; Nielsen, John B; Mouritsen, Lone; Sørensen, Michael; Lose, Gunnar

    2008-06-01

    BACKGROUND Polyacrylamide hydrogel (PAAG) is a nondegradable water-based polymer with high viscoelasticity. The gel is used as a tissue filler, the only risk being prolonged infection with anaerobic, contaminating microorganisms if not treated early with broad-spectrum antibiotics. OBJECTIVE With silicone gel as reference, PAAG tissue integration and migration was studied in a longitudinal study of the pig. MATERIALS AND METHODS Forty-one pigs were used. PAAG and silicone gel were injected into mammary tissue, and PAAG was injected into urethral or bladder wall or the anal canal. Tissues and regional lymph nodes were examined at 1, 1(1/2), 3, 3(1/2), 6, 12, and 14 months, and other lymph nodes and organs were examined at 1, 6, 12, and 14 months. RESULTS PAAG was invaded by macrophages and giant cells that were gradually replaced by a network of fibrous tissue. Silicone gel was seen inside these cells or as large vacuoles, surrounded by a fibrous capsule. Regional lymph nodes contained PAAG only at 1 1/2 months and silicone gel at 12 months. CONCLUSION PAAG is a stable, viscoelastic bulking agent, which unlike silicone gel is slowly integrated within its host tissue via a thin fibrous network. Long-term risk of fibrosis and migration is minimal. PMID:18547185

  14. Superior hybrid hydrogels of polyacrylamide enhanced by bacterial cellulose nanofiber clusters.

    PubMed

    Yuan, Ningxiao; Xu, Lu; Zhang, Lu; Ye, Haowen; Zhao, Jianhao; Liu, Zhong; Rong, Jianhua

    2016-10-01

    Hybrid polyacrylamide/bacterial cellulose nanofiber clusters (PAM/BC) hydrogels with high strength, toughness and recoverability were synthesized by in situ polymerization of acrylamide monomer in BC nanofiber clusters suspension. The hybrid gels exhibited an extremely large elongation at break of 2200%, and a high fracture stress of 1.35MPa. Additionally, the original length of hydrogels could be recovered after releasing the tensile force. Compressive results showed that the PAM/BC hybrid gels could reach a strain of about 99% without break, and was able to completely recover its original shape immediately after releasing the compression force. The compressive stress at 99% reached as high as 30MPa. Nearly no hysteresis in cyclic compressive tests was observed with these hybrid gels. The FT-IR, XRD and TGA analysis showed that hydrogen bonds between the PAM chains and BC nanofiber clusters mainly contributed to the superior mechanical properties of hybrid hydrogels. The cell viability results suggested that PAM/BC hybrid hydrogel was benign for biomedical application. These PAM/BC hydrogels offer a great promise as biomaterials such as bone and cartilage repair materials. PMID:27287117

  15. Our strategy in complication management of augmentation mammaplasty with polyacrylamide hydrogel injection in 235 patients.

    PubMed

    Luo, Sheng-Kang; Chen, Gunang-Ping; Sun, Zhong-Shen; Cheng, Ning-Xin

    2011-06-01

    Polyacrylamide hydrogel (PAAG) was once widely used in breast augmentation in China. Although it had been banned for augmentation mammaplasty in 2006, a large number of patients whose breasts were augmented with the gel injection have continued to seek medical advice because of its complications. The clinical management of these complications has never been standardised. The data of a total of 235 patients with complications following PAAG-injected breast augmentation have been summarised and the types and causations analysed. Magnetic resonance imaging (MRI) was undertaken in 228 patients with palpable masses, breast pain or tenderness, asymmetry or deformity and functional or psychological problems to eliminate neoplasm, infection and to delineate the diseases. The surgical gel evacuation via periareolar incisions was performed for all patients and immediate silicone breast prostheses were implanted in 108 patients and were delayed in 28 cases by 6 months. Most patients (214/235) of the group were satisfied with the treatment, and symptoms disappeared after removal of the gel. The gel distribution and involved tissue were well defined and neoplasm was ruled out by MRI. Postoperative MRI in 68 patients revealed that no obvious PAAG remaining. In either immediate or delayed reconstructive patients with silicone breast implants, good breast contour presented. A diagnosis and management strategy for these complications is proposed. In conclusion, the breast masses, pain and deformity are major complications after PAAG-injected breast augmentation. Psychological problems should be paid attention to. MRI is a sensitive and accurate method for diagnosis and treatment evaluation. Surgical removal of injected gel is the preferred method for complication management. The implantation of silicone prostheses for breast contour restoration after PAAG evacuation is effective for patients under strict selection. Our strategy for treating PAAG-related complications proved useful

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

    PubMed

    Ream, Jennifer A; Lewis, L Kevin; Lewis, Karen A

    2016-10-15

    Interactions between proteins and nucleic acids are frequently analyzed using electrophoretic mobility shift assays (EMSAs). This technique separates bound protein:nucleic acid complexes from free nucleic acids by electrophoresis, most commonly using polyacrylamide gels. The current study utilizes recent advances in agarose gel electrophoresis technology to develop a new EMSA protocol that is simpler and faster than traditional polyacrylamide methods. Agarose gels are normally run at low voltages (∼10 V/cm) to minimize heating and gel artifacts. In this study we demonstrate that EMSAs performed using agarose gels can be run at high voltages (≥20 V/cm) with 0.5 × TB (Tris-borate) buffer, allowing for short run times while simultaneously yielding high band resolution. Several parameters affecting band and image quality were optimized for the procedure, including gel thickness, agarose percentage, and applied voltage. Association of the siRNA-binding protein p19 with its target RNA was investigated using the new system. The agarose gel and conventional polyacrylamide gel methods generated similar apparent binding constants in side-by-side experiments. A particular advantage of the new approach described here is that the short run times (5-10 min) reduce opportunities for dissociation of bound complexes, an important concern in non-equilibrium nucleic acid binding experiments. PMID:27495142

  17. 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

  18. 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). PMID:27251892

  19. NKG2D ligands as therapeutic targets

    PubMed Central

    Spear, Paul; Wu, Ming-Ru; Sentman, Marie-Louise; Sentman, Charles L.

    2013-01-01

    The Natural Killer Group 2D (NKG2D) receptor plays an important role in protecting the host from infections and cancer. By recognizing ligands induced on infected or tumor cells, NKG2D modulates lymphocyte activation and promotes immunity to eliminate ligand-expressing cells. Because these ligands are not widely expressed on healthy adult tissue, NKG2D ligands may present a useful target for immunotherapeutic approaches in cancer. Novel therapies targeting NKG2D ligands for the treatment of cancer have shown preclinical success and are poised to enter into clinical trials. In this review, the NKG2D receptor and its ligands are discussed in the context of cancer, infection, and autoimmunity. In addition, therapies targeting NKG2D ligands in cancer are also reviewed. PMID:23833565

  20. Laser CT evaluation on normoxic PAGAT gel dosimeter

    NASA Astrophysics Data System (ADS)

    Kumar, D. S.; Samuel, E. J. J.; Watanabe, Y.

    2013-06-01

    Optical computed tomography has been shown to be a potentially useful imaging tool for the radiation therapy physicists. In radiation therapy, researchers have used optical CT for the readout of 3D dosimeters. The purpose of this paper is to describe the initial evaluation of a newly fabricated laser CT scanner for 3D gel dosimetry which works using the first generation principle. A normoxic PAGAT (Polyacrylamide Gelatin and Tetrakis) gel is used as a dosimeter for this analysis. When a laser passes through the gel phantom, absorption and scattering of photon take place. The optical attenuation coefficient of the laser can be obtained by measuring its intensity after passing through the gel by a sensor. The scanner motion is controlled by a computer program written in Microsoft Visual C++. Reconstruction and data analysis on the irradiated gel phantom is performed by suitable algorithm using Matlab software.

  1. Gel mobility shift assays to detect protein-RNA interactions.

    PubMed

    Yakhnin, Alexander V; Yakhnin, Helen; Babitzke, Paul

    2012-01-01

    The gel mobility shift assay is a powerful technique for detecting and quantifying protein-RNA interactions. While other techniques such as filter binding and isothermal titration calorimetry (ITC) are available for quantifying protein-RNA interactions, gel shift analysis provides the added advantage that you can visualize the protein-RNA complexes. In the gel shift assay, protein-RNA complexes are typically separated from the unbound RNA using native polyacrylamide gels in Tris/borate/EDTA buffer, although an alternative Tris-glycine buffering system is superior in many situations. Here, we describe both gel shift methods, along with strategies to improve separation of protein-RNA complexes from free RNA, which can be a particular challenge for small RNA binding proteins. PMID:22736005

  2. Site blocking effects on adsorbed polyacrylamide conformation

    NASA Astrophysics Data System (ADS)

    Brotherson, Brett A.

    ionic strength, and an adsorbed polymer on a surface functionalized with site blocking additives. This work investigated these scenarios using a low charge density high molecular weight cationic polyacrylamide. Three different substrates, for polymer adsorption were analyzed: mica, anionic latex, and glass. It was determined that, similar to previous studies, the adsorbed polymer layer thickness in water is relatively small even for high molecular weight polymers, on the order of tens of nanometers. The loop length distribution of a single polymer, experimentally verified for the first time, revealed a broad span of loop lengths as high as 1.5 microns. However, the bulk of the distribution was found between 40 and 260 nanometers. For the first time, previous theoretical predictions regarding the salt effect on adsorbed polymer conformation were confirmed experimentally. It was determined that the adsorbed polymer layer thickness expanded with increasing ionic strength of the solvent. Using atomic force microscopy, it was determined that the adsorbed polymer loop lengths and tail lengths increased with increasing ionic strength, supporting the results found using dynamic light scattering. The effect of the addition of site blocking additives on a single polymer's conformation was investigated for the first time. It was determined that the addition of site blocking additives caused strikingly similar results as the addition of salt to the medium. The changes in adsorbed polymer's loop lengths was found to be inconsistent and minimal. However, the changes in an adsorbed polymer's free tail length was found to increase with increasing site blocking additive levels. These results were obtained using either PDADMAC or cationic nanosilica as site blocking additives.

  3. Perspectives for spintronics in 2D materials

    NASA Astrophysics Data System (ADS)

    Han, Wei

    2016-03-01

    The past decade has been especially creative for spintronics since the (re)discovery of various two dimensional (2D) materials. Due to the unusual physical characteristics, 2D materials have provided new platforms to probe the spin interaction with other degrees of freedom for electrons, as well as to be used for novel spintronics applications. This review briefly presents the most important recent and ongoing research for spintronics in 2D materials.

  4. Effect of κ-carrageenan on volume phase transition for polyacrylamide (PAAm) hydrogel using the fluorescence technique

    NASA Astrophysics Data System (ADS)

    Aktaş, Demet Kaya

    2014-03-01

    Steady-state fluorescence (SSF) technique was employed for studying swelling of polyacrylamide (PAAm) gels with various content of κ-carrageenan ( κC). Disc shaped composite hydrogels were prepared by free-radical crosslinking copolymerization of acrylamide (AAm) with various amounts κC. N, N'-methylenebis (acrylamide) (BIS) and ammonium persulfate (APS) were used as crosslinker and initiator, respectively. Pyranine was introduced as a fluorescence probe. Fluorescence intensity of pyranine was monitored during in situ swelling processes of composite gels. It was observed that fluorescence intensity values decreased as swelling is proceeded. Li-Tanaka equation was used to determine the swelling time constants, τ and cooperative diffusion coefficients, D from intensity variations during the swelling processes. It was shown that swelling time constants, τ decreased and diffusion coefficients, D increased as the κC content in the composites are increased.

  5. Annotated Bibliography of EDGE2D Use

    SciTech Connect

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  6. Staring 2-D hadamard transform spectral imager

    DOEpatents

    Gentry, Stephen M.; Wehlburg, Christine M.; Wehlburg, Joseph C.; Smith, Mark W.; Smith, Jody L.

    2006-02-07

    A staring imaging system inputs a 2D spatial image containing multi-frequency spectral information. This image is encoded in one dimension of the image with a cyclic Hadamarid S-matrix. The resulting image is detecting with a spatial 2D detector; and a computer applies a Hadamard transform to recover the encoded image.

  7. Absolute absorption spectra of batho- and photorhodopsins at room temperature. Picosecond laser photolysis of rhodopsin in polyacrylamide.

    PubMed Central

    Kandori, H; Shichida, Y; Yoshizawa, T

    1989-01-01

    Picosecond laser photolysis of rhodopsin in 15% polyacrylamide gel was performed for estimating absolute absorption spectra of the primary intermediates of cattle rhodopsin (bathorhodopsin and photorhodopsin). Using a rhodopsin digitonin extract embedded in 15% polyacrylamide gel, a precise percentage of bleaching of rhodopsin after excitation of a picosecond laser pulse was measured. Using this value, the absolute absorption spectrum of bathorhodopsin was calculated from the spectral change before and 1 ns after the picosecond laser excitation (corresponding to the difference spectrum between rhodopsin and bathorhodopsin). The absorption spectrum of bathorhodopsin thus obtained displayed a lambda max at 535 nm, which was shorter than that at low temperature (543 nm) and a half band-width broader than that measured at low temperature. The oscillator strength of bathorhodopsin at room temperature was smaller than that at low temperature. The absolute absorption spectrum of photorhodopsin was also estimated from the difference spectrum measured at 15 ps after the excitation of rhodopsin (Shichida, Y., S. Matuoka, and T. Yoshizawa. 1984. Photobiochem. Photobiophys. 7:221-228), assuming a sequential conversion of photorhodopsin to bathorhodopsin. Its lambda max was located at approximately 570 nm, and the oscillator strength was smaller than those of rhodopsin and bathorhodopsin. PMID:2790133

  8. 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.

  9. 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.

  10. 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

  11. Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry.

    PubMed

    Singh, Pramod Kumar; Shrivastava, Nidhi; Chaturvedi, Krishna; Sharma, Bechan; Bhagyawant, Sameer S

    2016-01-01

    Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0-10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana. PMID:27144024

  12. Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

    PubMed Central

    Singh, Pramod Kumar; Shrivastava, Nidhi; Chaturvedi, Krishna

    2016-01-01

    Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana. PMID:27144024

  13. Aerosol gels

    NASA Technical Reports Server (NTRS)

    Sorensen, Christopher M. (Inventor); Chakrabarti, Amitabha (Inventor); Dhaubhadel, Rajan (Inventor); Gerving, Corey (Inventor)

    2010-01-01

    An improved process for the production of ultralow density, high specific surface area gel products is provided which comprises providing, in an enclosed chamber, a mixture made up of small particles of material suspended in gas; the particles are then caused to aggregate in the chamber to form ramified fractal aggregate gels. The particles should have a radius (a) of up to about 50 nm and the aerosol should have a volume fraction (f.sub.v) of at least 10.sup.-4. In preferred practice, the mixture is created by a spark-induced explosion of a precursor material (e.g., a hydrocarbon) and oxygen within the chamber. New compositions of matter are disclosed having densities below 3.0 mg/cc.

  14. POLYACRYLAMIDE (PAM) IN AGRICULTURE AND ENVIRONMENTAL LAND MANAGEMENT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Anionic polyacrylamide (PAM) has been sold since 1995 to reduce irrigation-induced erosion and enhance infiltration. Its soil stabilizing and flocculating properties improve runoff water quality by reducing sediments, N, dissolved reactive P (DRP) and total P, chemical oxygen demand (COD), pesticid...

  15. 40 CFR 721.10700 - Polyfluorinated alkyl thio polyacrylamide (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Polyfluorinated alkyl thio polyacrylamide (generic). 721.10700 Section 721.10700 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances...

  16. PREPARATION OF STARCH-GRAFT-POLYACRYLAMIDE COPOLYMERS BY REACTIVE EXTRUSION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Graft copolymers of starch and polyacrylamide (PAAm) were prepared by reactive extrusion using a co-rotating twin screw extruder and ammonium persulfate initiator. Feed rates were 109 g/min to 325 g/min (all components) at a moisture content of 50%, with screw speeds in the range 100 rpm to 300 rpm...

  17. 21 CFR 173.10 - Modified polyacrylamide resin.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Modified polyacrylamide resin. 173.10 Section 173.10 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) SECONDARY DIRECT FOOD ADDITIVES PERMITTED IN FOOD FOR HUMAN CONSUMPTION Polymer Substances and...

  18. Polyacrylamide molecular weight effects on soil infiltration and erosion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seal formation at the surface of smectitic 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. HRP-Mediated Synthesis of Starch-Polyacrylamide Graft Copolymers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Modified starch-based polymers can be engineered for specific properties by combining starch with synthetic polymers through graft copolymerization. Polyacrylamide grafted starches have received a great deal of applications in areas such as superabsorbent paper-making additives, drag reduction and ...

  20. HRP-Mediated Synthesis of Starch-Polyacrylamide Graft Copolymers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Modified starch-based polymers can be engineered for specific properties by combining starch with synthetic polymers through graft copolymerization. Polyacrylamide grafted starch have received a great deal of applications in areas such as superabsorbent paper-making additives, drag reduction and te...

  1. Acrylamide monomer leaching from polyacrylamide-treated irrigation furrows

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Water-soluble polyacrylamide (WSPAM), used to reduce erosion in furrow irrigated fields and other agriculture applications, contain less than 0.05% Acrylamide monomer (AMD). The AMD, a potent neurotoxicant and suspected carcinogen, is readily dissolved and transported in flowing water. Deep percol...

  2. PREPARATION OF STARCH-G-POLYACRYLAMIDE COPOLYMERS BY REACTIVE EXTRUSION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Graft copolymers of starch and polyacrylamide were prepared by reactive extrusion using a co-rotating twin screw extruder and ammonium persulfate initiator. Feed rates were 109 g/min up to 325 g/min (all components) at a moisture content of 50 percent, with screw speeds in the range 100 rpm to 300 ...

  3. A study on patients treated with polyacrylamide hydrogel injection for facial corrections.

    PubMed

    Breiting, Vibeke; Aasted, Annet; Jørgensen, Anna; Opitz, Per; Rosetzsky, Allan

    2004-01-01

    Polyacrylamide hydrogel (PAAG) has been used as a tissue filler in facial corrective surgery and for breast augmentation in Kiev, Ukraine, for more than 10 years with reportedly very good results. These results, however, have not been published in peer-reviewed journals. A Danish/Swedish group of plastic surgeons with special interest in facial corrective surgery did a retrospective, systematic, pre-planned investigation of 104 patients treated at the center in Kiev. All data were entered into a pre-programmed database for data processing. The mean age of this population was 37.4 years and the mean time since the gel injection was 3.9 years. An average of 5.7 ml of PAAG was injected prior to the investigation. The gel was well tolerated and assessment of the outcome was judged to be very good by 78% and good by 22%, by both physicians and patients. It is concluded that PAAG is well tolerated and seems to be a promising product for facial corrective surgery. Currently, the product (Aquamid) is being studied in several prospective clinical trials, one of which is completed and in the process of preparation for publication. PMID:15116275

  4. A LOW-COST HIGH THROUGHPUT POLYACRYLAMIDE GEL ELECTROPHORESIS SYSTEM FOR GENOTYPING WITH MICROSATELLITE DNA MARKERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite DNA markers are widely used in genetic research but the genotyping cost with this marker system is high and the throughput is limited with conventional methods. The objective of this paper is to introduce a low-cost, high-throughput system developed in our laboratories for the detect...

  5. A preparation of Alzheimer paired helical filaments that displays distinct tau proteins by polyacrylamide gel electrophoresis.

    PubMed Central

    Greenberg, S G; Davies, P

    1990-01-01

    Paired helical filaments (PHFs) are prominent components of Alzheimer disease (AD) neurofibrillary tangles (NFTs). Rather than isolating NFTs, we selected for PHF populations that can be extracted from AD brain homogenates. About 50% of PHF immunoreactivity can be obtained in 27,200 x g supernatants following homogenization in buffers containing 0.8 M NaCl. We further enriched for PHFs by taking advantage of their insolubility in the presence of zwitterionic detergents and 2-mercaptoethanol, removal of aggregates by filtration through 0.45-microns filters, and sucrose density centrifugation. PHF-enriched fractions contained two to five proteins of 57-68 kDa that displayed the same antigenic properties as PHFs. Since the 57- to 68-kDa PHF proteins are antigenically related to tau proteins, they are similar to the tau proteins previously observed in NFTs. However, further analysis revealed that PHF-associated tau can be distinguished from normal, soluble tau by PHF antibodies that do not recognize human adult tau and by one- and two-dimensional PAGE. Images PMID:2116006

  6. Identification of peanut hybrids using microsatellite markers and horizontal polyacrylamide gel electrophoresis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In peanut hybridization, it is very important to be able to distinguish selfs from true hybrids to save time and resources. To help facilitate this effort and provide molecular distinction between selfs from hybrids, DNA was extracted from leaf tissue of F1 or F2 plants, and SSR markers were amplif...

  7. Light field morphing using 2D features.

    PubMed

    Wang, Lifeng; Lin, Stephen; Lee, Seungyong; Guo, Baining; Shum, Heung-Yeung

    2005-01-01

    We present a 2D feature-based technique for morphing 3D objects represented by light fields. Existing light field morphing methods require the user to specify corresponding 3D feature elements to guide morph computation. Since slight errors in 3D specification can lead to significant morphing artifacts, we propose a scheme based on 2D feature elements that is less sensitive to imprecise marking of features. First, 2D features are specified by the user in a number of key views in the source and target light fields. Then the two light fields are warped view by view as guided by the corresponding 2D features. Finally, the two warped light fields are blended together to yield the desired light field morph. Two key issues in light field morphing are feature specification and warping of light field rays. For feature specification, we introduce a user interface for delineating 2D features in key views of a light field, which are automatically interpolated to other views. For ray warping, we describe a 2D technique that accounts for visibility changes and present a comparison to the ideal morphing of light fields. Light field morphing based on 2D features makes it simple to incorporate previous image morphing techniques such as nonuniform blending, as well as to morph between an image and a light field. PMID:15631126

  8. 2D materials for nanophotonic devices

    NASA Astrophysics Data System (ADS)

    Xu, Renjing; Yang, Jiong; Zhang, Shuang; Pei, Jiajie; Lu, Yuerui

    2015-12-01

    Two-dimensional (2D) materials have become very important building blocks for electronic, photonic, and phononic devices. The 2D material family has four key members, including the metallic graphene, transition metal dichalcogenide (TMD) layered semiconductors, semiconducting black phosphorous, and the insulating h-BN. Owing to the strong quantum confinements and defect-free surfaces, these atomically thin layers have offered us perfect platforms to investigate the interactions among photons, electrons and phonons. The unique interactions in these 2D materials are very important for both scientific research and application engineering. In this talk, I would like to briefly summarize and highlight the key findings, opportunities and challenges in this field. Next, I will introduce/highlight our recent achievements. We demonstrated atomically thin micro-lens and gratings using 2D MoS2, which is the thinnest optical component around the world. These devices are based on our discovery that the elastic light-matter interactions in highindex 2D materials is very strong. Also, I would like to introduce a new two-dimensional material phosphorene. Phosphorene has strongly anisotropic optical response, which creates 1D excitons in a 2D system. The strong confinement in phosphorene also enables the ultra-high trion (charged exciton) binding energies, which have been successfully measured in our experiments. Finally, I will briefly talk about the potential applications of 2D materials in energy harvesting.

  9. Inertial solvation in femtosecond 2D spectra

    NASA Astrophysics Data System (ADS)

    Hybl, John; Albrecht Ferro, Allison; Farrow, Darcie; Jonas, David

    2001-03-01

    We have used 2D Fourier transform spectroscopy to investigate polar solvation. 2D spectroscopy can reveal molecular lineshapes beneath ensemble averaged spectra and freeze molecular motions to give an undistorted picture of the microscopic dynamics of polar solvation. The transition from "inhomogeneous" to "homogeneous" 2D spectra is governed by both vibrational relaxation and solvent motion. Therefore, the time dependence of the 2D spectrum directly reflects the total response of the solvent-solute system. IR144, a cyanine dye with a dipole moment change upon electronic excitation, was used to probe inertial solvation in methanol and propylene carbonate. Since the static Stokes' shift of IR144 in each of these solvents is similar, differences in the 2D spectra result from solvation dynamics. Initial results indicate that the larger propylene carbonate responds more slowly than methanol, but appear to be inconsistent with rotational estimates of the inertial response. To disentangle intra-molecular vibrations from solvent motion, the 2D spectra of IR144 will be compared to the time-dependent 2D spectra of the structurally related nonpolar cyanine dye HDITCP.

  10. Internal Photoemission Spectroscopy of 2-D Materials

    NASA Astrophysics Data System (ADS)

    Nguyen, Nhan; Li, Mingda; Vishwanath, Suresh; Yan, Rusen; Xiao, Shudong; Xing, Huili; Cheng, Guangjun; Hight Walker, Angela; Zhang, Qin

    Recent research has shown the great benefits of using 2-D materials in the tunnel field-effect transistor (TFET), which is considered a promising candidate for the beyond-CMOS technology. The on-state current of TFET can be enhanced by engineering the band alignment of different 2D-2D or 2D-3D heterostructures. Here we present the internal photoemission spectroscopy (IPE) approach to determine the band alignments of various 2-D materials, in particular SnSe2 and WSe2, which have been proposed for new TFET designs. The metal-oxide-2-D semiconductor test structures are fabricated and characterized by IPE, where the band offsets from the 2-D semiconductor to the oxide conduction band minimum are determined by the threshold of the cube root of IPE yields as a function of photon energy. In particular, we find that SnSe2 has a larger electron affinity than most semiconductors and can be combined with other semiconductors to form near broken-gap heterojunctions with low barrier heights which can produce a higher on-state current. The details of data analysis of IPE and the results from Raman spectroscopy and spectroscopic ellipsometry measurements will also be presented and discussed.

  11. In-gel staining of proteins in native poly acryl amide gel electrophoresis using tetrakis(4-sulfonato phenyl)porphyrin.

    PubMed

    Divakar, Kalivarathan; Sujatha, Vijayan; Barath, Sridhar; Srinath, Krishnamurthy; Gautam, Pennathur

    2011-01-01

    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. We have developed a method for direct visualization of protein bands in PAGE using tetrakis(4-sulfonato phenyl)porphyrin (TPPS) as a dye without the need for any post electrophoretic steps, where separation and recovery of enzymes become much easier for further analysis. Activity staining was done to prove that the biochemical activity of the enzymes was preserved after electrophoresis. PMID:21233569

  12. Brittle damage models in DYNA2D

    SciTech Connect

    Faux, D.R.

    1997-09-01

    DYNA2D is an explicit Lagrangian finite element code used to model dynamic events where stress wave interactions influence the overall response of the system. DYNA2D is often used to model penetration problems involving ductile-to-ductile impacts; however, with the advent of the use of ceramics in the armor-anti-armor community and the need to model damage to laser optics components, good brittle damage models are now needed in DYNA2D. This report will detail the implementation of four brittle damage models in DYNA2D, three scalar damage models and one tensor damage model. These new brittle damage models are then used to predict experimental results from three distinctly different glass damage problems.

  13. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-01-01

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  14. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-12-31

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  15. 2D electronic materials for army applications

    NASA Astrophysics Data System (ADS)

    O'Regan, Terrance; Perconti, Philip

    2015-05-01

    The record electronic properties achieved in monolayer graphene and related 2D materials such as molybdenum disulfide and hexagonal boron nitride show promise for revolutionary high-speed and low-power electronic devices. Heterogeneous 2D-stacked materials may create enabling technology for future communication and computation applications to meet soldier requirements. For instance, transparent, flexible and even wearable systems may become feasible. With soldier and squad level electronic power demands increasing, the Army is committed to developing and harnessing graphene-like 2D materials for compact low size-weight-and-power-cost (SWAP-C) systems. This paper will review developments in 2D electronic materials at the Army Research Laboratory over the last five years and discuss directions for future army applications.

  16. 2-d Finite Element Code Postprocessor

    1996-07-15

    ORION is an interactive program that serves as a postprocessor for the analysis programs NIKE2D, DYNA2D, TOPAZ2D, and CHEMICAL TOPAZ2D. ORION reads binary plot files generated by the two-dimensional finite element codes currently used by the Methods Development Group at LLNL. Contour and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forcesmore » along constrained boundaries, and momentum. ORION has been applied to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.« less

  17. Measurements of elastic moduli of silicone gel substrates with a microfluidic device.

    PubMed

    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

  18. 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

  19. Chemical Approaches to 2D Materials.

    PubMed

    Samorì, Paolo; Palermo, Vincenzo; Feng, Xinliang

    2016-08-01

    Chemistry plays an ever-increasing role in the production, functionalization, processing and applications of graphene and other 2D materials. This special issue highlights a selection of enlightening chemical approaches to 2D materials, which nicely reflect the breadth of the field and convey the excitement of the individuals involved in it, who are trying to translate graphene and related materials from the laboratory into a real, high-impact technology. PMID:27478083

  20. Extended 2D generalized dilaton gravity theories

    NASA Astrophysics Data System (ADS)

    de Mello, R. O.

    2008-09-01

    We show that an anomaly-free description of matter in (1+1) dimensions requires a deformation of the 2D relativity principle, which introduces a non-trivial centre in the 2D Poincaré algebra. Then we work out the reduced phase space of the anomaly-free 2D relativistic particle, in order to show that it lives in a noncommutative 2D Minkowski space. Moreover, we build a Gaussian wave packet to show that a Planck length is well defined in two dimensions. In order to provide a gravitational interpretation for this noncommutativity, we propose to extend the usual 2D generalized dilaton gravity models by a specific Maxwell component, which guages the extra symmetry associated with the centre of the 2D Poincaré algebra. In addition, we show that this extension is a high energy correction to the unextended dilaton theories that can affect the topology of spacetime. Further, we couple a test particle to the general extended dilaton models with the purpose of showing that they predict a noncommutativity in curved spacetime, which is locally described by a Moyal star product in the low energy limit. We also conjecture a probable generalization of this result, which provides strong evidence that the noncommutativity is described by a certain star product which is not of the Moyal type at high energies. Finally, we prove that the extended dilaton theories can be formulated as Poisson Sigma models based on a nonlinear deformation of the extended Poincaré algebra.

  1. The use of high field strength and parallel imaging techniques for MRI-based gel dosimetry in stereotactic radiosurgery

    NASA Astrophysics Data System (ADS)

    Seimenis, I.; Moutsatsos, A.; Petrokokkinos, L.; Kantemiris, I.; Benekos, O.; Efstathopoulos, E.; Papagiannis, P.; Spevacek, V.; Semnicka, J.; Dvorak, P.

    2009-07-01

    The poor clinical acceptance of polymer gel dosimetry for dose verification in stereotactic radio-surgery applications stems, inter alia, from the increased MRI acquisition times needed to meet the associated spatial resolution demands. To examine whether this could be partly alleviated by the employment of 3 Tesla imagers and parallel imaging techniques, a PolyAcrylamide Gel filled tube was irradiated in a Leksell Gamma Knife unit with two single irradiation shots (4 mm and 8 mm) and underwent four different scanning sessions using an optimised, volume selective, 32 echo CPMG pulse sequence: One performed on a 1.5 T imager with 0.5 × 0.5 mm2 in-plane spatial resolution and 0.75 mm slice thickness (scan A), while the rest three on a 3.0 T imager; one with the same spatial resolution as in scan A (scan B) and two with finer in-plane resolution (scans C and D). In scans B and C the sensitivity encoding (SENSE) parallel imaging technique was employed. Relative dose distributions derived by scan A were benchmarked against Monte Carlo and treatment planning system calculations, and then used as the reference for the comparison of 2D relative dose distributions derived by each scan in terms of dose difference and distance-to-agreement criteria (γ index tool). Findings suggest that careful MRI planning based on a figure of merit accounting for scanning time and precision for a given increase in spatial resolution, could facilitate the introduction of polymer gel dosimetry into the clinical setting as a practical quality assurance tool for complex radio-surgery techniques.

  2. Recycling of superfine resolution agarose gel.

    PubMed

    Seng, T-Y; Singh, R; Faridah, Q Z; Tan, S-G; Alwee, S S R S

    2013-01-01

    Genetic markers are now routinely used in a wide range of applications, from forensic DNA analysis to marker-assisted plant and animal breeding. The usual practice in such work is to extract the DNA, prime the markers of interest, and sift them out by electrically driving them through an appropriate matrix, usually a gel. The gels, made from polyacrylamide or agarose, are of high cost, limiting their greater applications in molecular marker work, especially in developing countries where such technology has great potential. Trials using superfine resolution (SFR) agarose for SSR marker screening showed that it is capable of resolving SSR loci and can be reused up to 14 times, thus greatly reducing the cost of each gel run. Furthermore, for certain applications, low concentrations of agarose sufficed and switching to lithium borate buffer, instead of the conventional Tris-borate-ethylenediaminetetraacetic acid buffer, will further save time and cost. The 2.5% gel was prepared following the Agarose SFR(TM) manual by adding 2.5 g agarose powder into 100 mL 1X lithium borate buffer in a 250-mL flask with rapid stirring. Two midigels (105 x 83 mm, 17 wells) or 4 minigels (50 x 83 mm, 8 wells), 4 mm thickness can be prepared from 100 mL gel solution. A total of 1680 PCR products amplified using 140 SSR markers from oil palm DNA samples were tested in this study using SFR recycled gel. As average, the gel can be recycled 8 times with good resolution, but can be recycled up to 14 times before the resolutions get blurred. PMID:23546970

  3. Formation of microemulsion: Effect of temperature and polyacrylamide

    SciTech Connect

    John, A.C.; Rakshit, A.K. )

    1993-03-01

    The pseudoternary phase diagram of the system involving cyclohexane, sodium dodecyl sulphate, propanol, and water was constructed for an SDS-to-propanol mass ratio 1:2. The area of the monophasic microemulsion region was computed. The effects of change of temperature and change of concentration of water-soluble polyacrylamide (PAA) on the microemulsion zone as well as the conductance, viscosity, and adiabatic compressibility of the microemulsion systems were studied. It was observed that for the water system there is a critical temperature below which the microemulsion zone increases with temperature, though at higher temperature the zone decreases within the range studied. The effects of presence of polyacrylamide above and below 0.003%(w/v)also are different from each other.

  4. Polyacrylamide soft tissue filler nodule mimicking a mucoepidermoid carcinoma.

    PubMed

    Karagozoglu, K H; van der Waal, I

    2008-06-01

    A 39-year-old woman is described in whom histopathologic examination of a nodule of the cheek mucosa was suggestive of a mucoepidermoid carcinoma. Only after the availability of a wider surgical specimen was a distinct foreign body reaction to polyacrylamide soft tissue filler observed. On inquiry, the patient admitted to having this filler injected into her nasolabial folds 3 years previously. PMID:18313268

  5. Immobilization of enzymes on alginic acid-polyacrylamide copolymers

    SciTech Connect

    Kumaraswamy, M.D.K.; Panduranga R.K.; Thomas J.K.; Santappa, M.

    1981-08-01

    In this report, the authors present initial results and limitations of a polymeric system for the immobilization of enzymes. Enzymes attached to insoluble polymers of natural and synthetic origin are gaining importance in many industrial and biomedical applications. Graft copolymers are used as enzyme supports and in this study a novel polymeric system of alginic acid-polyacrylamide graft copolymer is described which was used for immobilizing enzymes. (Refs. 4).

  6. Optical modulators with 2D layered materials

    NASA Astrophysics Data System (ADS)

    Sun, Zhipei; Martinez, Amos; Wang, Feng

    2016-04-01

    Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that 2D layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this Review, we cover the state of the art of optical modulators based on 2D materials, including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as 2D heterostructures, plasmonic structures, and silicon and fibre integrated structures. We also take a look at the future perspectives and discuss the potential of yet relatively unexplored mechanisms, such as magneto-optic and acousto-optic modulation.

  7. Large Area Synthesis of 2D Materials

    NASA Astrophysics Data System (ADS)

    Vogel, Eric

    Transition metal dichalcogenides (TMDs) have generated significant interest for numerous applications including sensors, flexible electronics, heterostructures and optoelectronics due to their interesting, thickness-dependent properties. Despite recent progress, the synthesis of high-quality and highly uniform TMDs on a large scale is still a challenge. In this talk, synthesis routes for WSe2 and MoS2 that achieve monolayer thickness uniformity across large area substrates with electrical properties equivalent to geological crystals will be described. Controlled doping of 2D semiconductors is also critically required. However, methods established for conventional semiconductors, such as ion implantation, are not easily applicable to 2D materials because of their atomically thin structure. Redox-active molecular dopants will be demonstrated which provide large changes in carrier density and workfunction through the choice of dopant, treatment time, and the solution concentration. Finally, several applications of these large-area, uniform 2D materials will be described including heterostructures, biosensors and strain sensors.

  8. 2D microwave imaging reflectometer electronics

    SciTech Connect

    Spear, A. G.; Domier, C. W. Hu, X.; Muscatello, C. M.; Ren, X.; Luhmann, N. C.; Tobias, B. J.

    2014-11-15

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  9. 2D microwave imaging reflectometer electronics

    NASA Astrophysics Data System (ADS)

    Spear, A. G.; Domier, C. W.; Hu, X.; Muscatello, C. M.; Ren, X.; Tobias, B. J.; Luhmann, N. C.

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  10. 2D microwave imaging reflectometer electronics.

    PubMed

    Spear, A G; Domier, C W; Hu, X; Muscatello, C M; Ren, X; Tobias, B J; Luhmann, N C

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program. PMID:25430247

  11. 2D-Crystal-Based Functional Inks.

    PubMed

    Bonaccorso, Francesco; Bartolotta, Antonino; Coleman, Jonathan N; Backes, Claudia

    2016-08-01

    The possibility to produce and process graphene, related 2D crystals, and heterostructures in the liquid phase makes them promising materials for an ever-growing class of applications as composite materials, sensors, in flexible optoelectronics, and energy storage and conversion. In particular, the ability to formulate functional inks with on-demand rheological and morphological properties, i.e., lateral size and thickness of the dispersed 2D crystals, is a step forward toward the development of industrial-scale, reliable, inexpensive printing/coating processes, a boost for the full exploitation of such nanomaterials. Here, the exfoliation strategies of graphite and other layered crystals are reviewed, along with the advances in the sorting of lateral size and thickness of the exfoliated sheets together with the formulation of functional inks and the current development of printing/coating processes of interest for the realization of 2D-crystal-based devices. PMID:27273554

  12. 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.

  13. The 2D lingual appliance system.

    PubMed

    Cacciafesta, Vittorio

    2013-09-01

    The two-dimensional (2D) lingual bracket system represents a valuable treatment option for adult patients seeking a completely invisible orthodontic appliance. The ease of direct or simplified indirect bonding of 2D lingual brackets in combination with low friction mechanics makes it possible to achieve a good functional and aesthetic occlusion, even in the presence of a severe malocclusion. The use of a self-ligating bracket significantly reduces chair-side time for the orthodontist, and the low-profile bracket design greatly improves patient comfort. PMID:24005953

  14. Inkjet printing of 2D layered materials.

    PubMed

    Li, Jiantong; Lemme, Max C; Östling, Mikael

    2014-11-10

    Inkjet printing of 2D layered materials, such as graphene and MoS2, has attracted great interests for emerging electronics. However, incompatible rheology, low concentration, severe aggregation and toxicity of solvents constitute critical challenges which hamper the manufacturing efficiency and product quality. Here, we introduce a simple and general technology concept (distillation-assisted solvent exchange) to efficiently overcome these challenges. By implementing the concept, we have demonstrated excellent jetting performance, ideal printing patterns and a variety of promising applications for inkjet printing of 2D layered materials. PMID:25169938

  15. Measurement of 2D birefringence distribution

    NASA Astrophysics Data System (ADS)

    Noguchi, Masato; Ishikawa, Tsuyoshi; Ohno, Masahiro; Tachihara, Satoru

    1992-10-01

    A new measuring method of 2-D birefringence distribution has been developed. It has not been an easy job to get a birefringence distribution in an optical element with conventional ellipsometry because of its lack of scanning means. Finding an analogy between the rotating analyzer method in ellipsometry and the phase-shifting method in recently developed digital interferometry, we have applied the phase-shifting algorithm to ellipsometry, and have developed a new method that makes the measurement of 2-D birefringence distribution easy and possible. The system contains few moving parts, assuring reliability, and measures a large area of a sample at one time, making the measuring time very short.

  16. Parallel stitching of 2D materials

    DOE PAGESBeta

    Ling, Xi; Wu, Lijun; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; et al

    2016-01-27

    Diverse parallel stitched 2D heterostructures, including metal–semiconductor, semiconductor–semiconductor, and insulator–semiconductor, are synthesized directly through selective “sowing” of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. Lastly, the methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  17. Parallel Stitching of 2D Materials.

    PubMed

    Ling, Xi; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; Hsu, Allen L; Bie, Yaqing; Lee, Yi-Hsien; Zhu, Yimei; Wu, Lijun; Li, Ju; Jarillo-Herrero, Pablo; Dresselhaus, Mildred; Palacios, Tomás; Kong, Jing

    2016-03-01

    Diverse parallel stitched 2D heterostructures, including metal-semiconductor, semiconductor-semiconductor, and insulator-semiconductor, are synthesized directly through selective "sowing" of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. The methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits. PMID:26813882

  18. Baby universes in 2d quantum gravity

    NASA Astrophysics Data System (ADS)

    Ambjørn, Jan; Jain, Sanjay; Thorleifsson, Gudmar

    1993-06-01

    We investigate the fractal structure of 2d quantum gravity, both for pure gravity and for gravity coupled to multiple gaussian fields and for gravity coupled to Ising spins. The roughness of the surfaces is described in terms of baby universes and using numerical simulations we measure their distribution which is related to the string susceptibility exponent γstring.

  19. Investigation on Tissue Equivalent Normoxic Polymer Gel Dosimeter using In-house Laser CT scanning system

    NASA Astrophysics Data System (ADS)

    Senthil Kumar, D.; Jebaseelan Samuel, E. James

    2010-11-01

    Optical Computed Tomography has wide applications in the treatment of cancer. In continuation of this, an in-house Laser CT scanner has been built for "3D gel dosimetry". The Laser CT (LCT) scanner plays a major for Gel dosimeter or phantom readout and in clinical radiation therapy as a 3-Dimensional Radiation Dosimetry. A gel dosimeter which absorbs dose in a tissue-equivalent manner and allows the measurement of spatial distribution of the deposited dose is required. The normoxic PAGAT (Polyacrylamide Gelatin and Tetrakis) gel is used as a dosimeter for this analysis. When laser passes through this gel phantom, absorption and scattering takes place and combined to attenuation. The optical attenuation coefficient of the laser can be obtained by measuring its intensity after passing through the gel by means of a sensor. Reconstruction using Mat Lab algorithm provides 3D dose distribution.

  20. Differential Analysis of 2-D Maps by Pixel-Based Approaches.

    PubMed

    Marengo, Emilio; Robotti, Elisa; Quasso, Fabio

    2016-01-01

    Two approaches to the analysis of 2-D maps are available: the first one involves a step of spot detection on each gel image; the second one is based instead on the direct differential analysis of 2-D map images, following a pixel-based procedure. Both approaches strongly depend on the proper alignment of the gel images, but the pixel-based approach allows to solve important drawbacks of the spot-volume procedure, i.e., the problem of missing data and of overlapping spots. However, this approach is quite computationally intensive and requires the use of algorithms able to separate the information (i.e., spot-related information) from the background. Here, the most recent pixel-based approaches are described. PMID:26611422

  1. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology

    PubMed Central

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-01-01

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct “beyond graphene” domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials. PMID:26861346

  2. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology.

    PubMed

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-01-01

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct "beyond graphene" domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials. PMID:26861346

  3. Calibration of laser tomography as a new optical diagnostic tool applied to dosimetric polymer gels

    NASA Astrophysics Data System (ADS)

    Alwan, R.; Guermeur, F.; Bailly, Y.; Simonin, L.; Svoboda, J.; Makovicka, L.; Martin, E.

    2008-03-01

    Numerous medical applications, as radiotherapy for example, require accurate and reproducible three-dimensional dose measurements with high spatial resolution. A solution of great interest and which has been exploited for many years is the use of dosimetric gels based on different physico-chemical principles, as Fricke's gels or polymer gels. Fricke's gels take advantage of the oxidation of ferrous ions in ferric while polymer gels are the result of the synthesis of polyacrylamide hydrogel from monomer and cross-linking agent. Fricke's gels have particular limitations not encountered with polymer gel dosimeters: the time delay between irradiation and measurement must be reduced in order to limit the diffusion of ferric ions which may remove the spatial dose information. That's why, during the past decade, many compositions of polymer gels have been studied (PAG, MAGIC, …), elaborated and even commercialized (BANG gels). However the gel composition remains of great interest regarding its physical properties. In this work, the authors propose a new optical diagnostic tool more flexible and less expensive in comparison with existing techniques like magnetic resonance imaging (MRI) and Optical-CT. This technique is based on light scattering behaviour occurring in an irradiated polymer gel (note that light scattering in Fricke's gels is very feeble, the latter being essentially absorbant).

  4. Isolation and Characterization of Polyacrylamide-Degrading Bacteria from Dewatered Sludge

    PubMed Central

    Yu, Feng; Fu, Ruimin; Xie, Yun; Chen, Wuling

    2015-01-01

    Polyacrylamide (PAM) is a water-soluble polymer that is widely used as a flocculant in sewage treatment. The accumulation of PAM affects the formation of dewatered sludge and potentially produces hazardous monomers. In the present study, the bacterial strain HI47 was isolated from dewatered sludge. This strain could metabolize PAM as its sole nutrient source and was subsequently identified as Pseudomonas putida. The efficiency of PAM degradation was 31.1% in 7 days and exceeded 45% under optimum culture condition (pH 7.2, 39 °C and 100 rpm). The addition of yeast extract and glucose improved the bacterial growth and PAM degradation. The degraded PAM samples were analyzed by gel-filtration chromatography, Fourier transform infrared and high-performance liquid chromatography. The results showed that high-molecular-weight PAM was partly cleaved to small molecular oligomer derivatives and part of the amide groups of PAM had been converted to carboxyl groups. The biodegradation did not accumulate acrylamide monomers. Based on the SDS-PAGE and N-terminal sequencing results, the PAM amide groups were converted into carboxyl groups by a PAM-induced extracellular enzyme from the aliphatic amidase family. PMID:25893998

  5. Effects of polymer concentration on the morphology of calcium phosphate crystals formed in polyacrylamide hydrogels

    NASA Astrophysics Data System (ADS)

    Yokoi, Taishi; Kawashita, Masakazu; Ohtsuki, Chikara

    2013-11-01

    Growing crystals in hydrogels is an attractive method to form inorganic solids with designed morphology under ambient conditions. Precipitation of the inorganic solids in a hydrogel matrix can be regarded as mimicking the process of biomineralization. In the construction of biominerals, an organic template composed of insoluble macromolecules is used to control the crystal growth of the inorganic compounds. The morphological control in biomineralization can be applied to artificial reaction systems. In this study, the morphology of calcium phosphate crystals formed in polymeric hydrogels of various polymer concentrations was investigated. Spherical octacalcium phosphate (OCP) precipitated in the polyacrylamide (PAAm) hydrogels. Fibrous crystals gradually covered the surface of the spherical crystals as the polymer concentration of the gel increased. The morphology of the OCP crystals changed from sea urchin shapes to wool-ball shapes with increasing PAAm concentration. The morphological change is generated by the template effect of the polymer wall, which is made up of stacked PAAm sheets, surrounding the spherical OCP crystals.

  6. Isolation and characterization of polyacrylamide-degrading bacteria from dewatered sludge.

    PubMed

    Yu, Feng; Fu, Ruimin; Xie, Yun; Chen, Wuling

    2015-04-01

    Polyacrylamide (PAM) is a water-soluble polymer that is widely used as a flocculant in sewage treatment. The accumulation of PAM affects the formation of dewatered sludge and potentially produces hazardous monomers. In the present study, the bacterial strain HI47 was isolated from dewatered sludge. This strain could metabolize PAM as its sole nutrient source and was subsequently identified as Pseudomonas putida. The efficiency of PAM degradation was 31.1% in 7 days and exceeded 45% under optimum culture condition (pH 7.2, 39 °C and 100 rpm). The addition of yeast extract and glucose improved the bacterial growth and PAM degradation. The degraded PAM samples were analyzed by gel-filtration chromatography, Fourier transform infrared and high-performance liquid chromatography. The results showed that high-molecular-weight PAM was partly cleaved to small molecular oligomer derivatives and part of the amide groups of PAM had been converted to carboxyl groups. The biodegradation did not accumulate acrylamide monomers. Based on the SDS-PAGE and N-terminal sequencing results, the PAM amide groups were converted into carboxyl groups by a PAM-induced extracellular enzyme from the aliphatic amidase family. PMID:25893998

  7. Multifunctional Biodegradable Polyacrylamide Nanocarriers for Cancer Theranostics - A “See and Treat” Strategy

    PubMed Central

    Wang, Shouyan; Kim, Gwangseong; Lee, Yong-Eun Koo; Hah, Hoe Jin; Ethirajan, Manivannan; Pandey, Ravindra K.; Kopelman, Raoul

    2012-01-01

    We describe here the development of multifunctional nanocarriers, based on amine functionalized biodegradable polyacrylamide nanoparticles (NPs), for cancer theranostics, including active tumor targeting, fluorescence imaging and photodynamic therapy. The structural design involves adding primary amino groups and biodegradable crosslinkers during the NP polymerization, while incorporating photodynamic and fluorescent imaging agents into the NP matrix, and conjugating PEG and tumor-targeting ligands onto the surface of the NPs. The as-synthesized NPs are spherical, with an average diameter of 44 nm. An accelerated biodegradation study, using sodium hydroxide or porcine liver esterase, indicated a hydrogel polymer matrix chain collapse within several days. By using gel permeation chromatography, small molecules were detected, after the degradation. In vitro targeting studies on human breast cancer cells indicate that the targeted NPs can be transported efficiently into tumor cells. Incubating the multifunctional nanocarriers into cancer cells enabled strong fluorescence imaging. Irradiation of the photosensitizing drug, incorporated within the NPs, with light of a suitable wavelength, causes significant but selective damage to the impregnated tumor cells, but only inside the illuminated areas. Overall, the potential of polymeric-based NPs as biodegradable, multifunctional nanocarriers, for cancer theranostics, is demonstrated here. PMID:22702416

  8. Rare earth oxide-doped titania nanocomposites with enhanced photocatalytic activity towards the degradation of partially hydrolysis polyacrylamide

    NASA Astrophysics Data System (ADS)

    Li, Jinhuan; Yang, Xia; Yu, Xiaodan; Xu, Leilei; Kang, Wanli; Yan, Wenhua; Gao, Hongfeng; Liu, Zhonghe; Guo, Yihang

    2009-01-01

    Rare-earth oxide-doped titania nanocomposites (RE 3+/TiO 2, where RE = Eu 3+, Pr 3+, Gd 3+, Nd 3+, and Y 3+) were prepared by a one-step sol-gel-solvothermal method. The products exhibited anatase phase structure, mesoporosity, and interesting surface compositions with three oxygen species and two titanium species. The products were used as the photocatalysts to degrade a partially hydrolysis polyacrylamide (HPAM) under UV-light irradiation, a very useful polymer in oil recovery. For comparison, Degussa P25 and as-prepared pure TiO 2 were also tested under the same conditions. The enhanced photocatalytic activity was obtained on as-prepared Eu 3+ (Gd 3+, Pr 3+)/TiO 2 composites, and the reasons were explained. Finally, the degradation pathway of HPAM over the RE 3+/TiO 2 composite was put forward based on the intermediates produced during the photocatalysis procedure.

  9. High-resolution gel dosimetry of a HDR brachytherapy source using normoxic polymer gel dosimeters: Preliminary study

    NASA Astrophysics Data System (ADS)

    Hurley, C.; McLucas, C.; Pedrazzini, G.; Baldock, C.

    2006-09-01

    Polymer gel dosimetry has been shown to be an effective tool in the analysis of radiotherapy treatments in cancer therapy, being used to map the dose distribution around an irradiation pattern of a polymer gel dosimeter. Combined with high-resolution magnetic resonance imaging (MRI), polymer gel dosimetry can be an effective dosimetry tool to map dose distributions with high spatial resolution (˜100 μm). Previously polyacrylamide polymer gel dosimetry required a strict hypoxic environment to protect the gel from oxygen infiltration as oxygen inhibits the polymerization reaction used to correlate to absorbed dose. However, with the advent of normoxic polymer gels, a strict hypoxic environment is not required. Normoxic polymer gel dosimeters can be manufactured under normal atmospheric conditions. This study assessed the use of a MAGIC normoxic polymer gel dosimeter to accurately map the dose distribution of a single-line irradiation and a point source irradiation from a brachytherapy radiation source administered through a nylon catheter inserted into the gel dosimeter. The phantoms were irradiated to a dose of 10 Gy at 2 mm from the source center and imaged using high-resolution MRI with an in-plane pixel size of 0.1055 mm/pixel. Good agreement was found between the dose points predicted by the computer treatment-planning system and the measured normalized dose profiles in the gel dosimeter. The use of normoxic polymer gel dosimeters with high-resolution MRI evaluation shows promise as an effective tool in applications requiring accurate dose distributions in high resolution, such as intravascular brachytherapy.

  10. Ti 3 C 2 T x (MXene)–polyacrylamide nanocomposite films

    DOE PAGESBeta

    Naguib, Michael; Saito, Tomonori; Lai, Sophia; Rager, Matthew S.; Aytug, Tolga; Parans Paranthaman, M.; Zhao, Meng-Qiang; Gogotsi, Yury

    2016-07-20

    Polymer nanocomposite films are of great interest due to their enhanced properties over base polymers. By incorporating 2D titanium carbide a representative of a new family of 2D materials, MXenes, as nanofillers into a water soluble polyacrylamide (PAM) matrix, the resulting films benefit from the flexibility, robustness, and processability of PAM, as well as the conductivity and mechanical properties of MXene fillers. We report on manufacturing and characterization of MXene-PAM nanocomposite films. Dimethylsulfoxide (DMSO) intercalation in-between the Ti3C2-based MXene layers led to full delamination of the MXene layers and hence a uniform dispersion of hydrophilic MXene nanosheets in aqueous PAMmore » solutions was achieved. Moreover, the polymer composite solutions of up to 75 wt.% MXene loading were sonicated and cast onto large Teflon trays and dried at room temperature to produce shiny black films. The observation of reduced 0002 peaks of Ti3C2Tx phase in X-ray diffraction patterns and TEM images indicate the presence of well dispersed nanoflakes. The as-prepared composite films are flexible and the conductivity was increased significantly to 3 x 10-3 S cm-1 for 6 wt. % MXene-PAM films. With high MXene loading, some non-uniformity between the top and bottom surfaces was observed. This could be due to the segregation of MXene layers in composite films during drying. Finally, the power law dependence of conductivity above the percolation threshold is presented through detailed conductivity measurements.« less

  11. Rapid DNA sequencing by horizontal ultrathin gel electrophoresis.

    PubMed Central

    Brumley, R L; Smith, L M

    1991-01-01

    A horizontal polyacrylamide gel electrophoresis apparatus has been developed that decreases the time required to separate the DNA fragments produced in enzymatic sequencing reactions. The configuration of this apparatus and the use of circulating coolant directly under the glass plates result in heat exchange that is approximately nine times more efficient than passive thermal transfer methods commonly used. Bubble-free gels as thin as 25 microns can be routinely cast on this device. The application to these ultrathin gels of electric fields up to 250 volts/cm permits the rapid separation of multiple DNA sequencing reactions in parallel. When used in conjunction with 32P-based autoradiography, the DNA bands appear substantially sharper than those obtained in conventional electrophoresis. This increased sharpness permits shorter autoradiographic exposure times and longer sequence reads. Images PMID:1870968

  12. Shape-Encoded Chitosan-Polyacrylamide Hybrid Hydrogel Microparticles with Controlled Macroporous Structures via Replica Molding for Programmable Biomacromolecular Conjugation.

    PubMed

    Kang, Eunae; Jung, Sukwon; Abel, John H; Pine, Allison; Yi, Hyunmin

    2016-05-31

    Polymeric hydrogel microparticle-based suspension arrays with shape-based encoding offer powerful alternatives to planar and bead-based arrays toward high throughput biosensing and medical diagnostics. We report a simple and robust micromolding technique for polyacrylamide- (PAAm-) based biopolymeric-synthetic hybrid microparticles with controlled 2D shapes containing a potent aminopolysaccharide chitosan as an efficient conjugation handle uniformly incorporated in PAAm matrix. A postfabrication conjugation approach utilizing amine-reactive chemistries on the chitosan shows stable incorporation and retained chemical reactivity of chitosan, readily tunable macroporous structures via simple addition of low content long-chain PEG porogens for improved conjugation capacity and kinetics, and one-pot biomacromolecular assembly via bioorthogonal click reactions with minimal nonspecific binding. We believe that the integrated fabrication-conjugation approach reported here could offer promising routes to programmable manufacture of hydrogel microparticle-based biomacromolecular conjugation and biofunctionalization platforms for a large range of applications. PMID:27191399

  13. Complications of polyacrylamide hydrogel (PAAG) injection in facial augmentation.

    PubMed

    Liu, H L; Cheung, W Y

    2010-01-01

    Polyacrylamide hydrogel (PAAG) has been used as an injectable filler for soft tissue augmentation for more than a decade. In recent years, PAAG has been advocated as a safe soft tissue filler for facial augmentation. However, the complications associated with PAAG injection in facial augmentation have not been widely covered in the literature. We present two cases of severe complications associated with PAAG injection in facial augmentation, including bony erosion and facial ulcer. Further studies are required to support the safety of PAAG in facial injection. PMID:19540824

  14. Static & Dynamic Response of 2D Solids

    1996-07-15

    NIKE2D is an implicit finite-element code for analyzing the finite deformation, static and dynamic response of two-dimensional, axisymmetric, plane strain, and plane stress solids. The code is fully vectorized and available on several computing platforms. A number of material models are incorporated to simulate a wide range of material behavior including elasto-placicity, anisotropy, creep, thermal effects, and rate dependence. Slideline algorithms model gaps and sliding along material interfaces, including interface friction, penetration and single surfacemore » contact. Interactive-graphics and rezoning is included for analyses with large mesh distortions. In addition to quasi-Newton and arc-length procedures, adaptive algorithms can be defined to solve the implicit equations using the solution language ISLAND. Each of these capabilities and more make NIKE2D a robust analysis tool.« less

  15. Stochastic Inversion of 2D Magnetotelluric Data

    2010-07-01

    The algorithm is developed to invert 2D magnetotelluric (MT) data based on sharp boundary parametrization using a Bayesian framework. Within the algorithm, we consider the locations and the resistivity of regions formed by the interfaces are as unknowns. We use a parallel, adaptive finite-element algorithm to forward simulate frequency-domain MT responses of 2D conductivity structure. Those unknown parameters are spatially correlated and are described by a geostatistical model. The joint posterior probability distribution function ismore » explored by Markov Chain Monte Carlo (MCMC) sampling methods. The developed stochastic model is effective for estimating the interface locations and resistivity. Most importantly, it provides details uncertainty information on each unknown parameter. Hardware requirements: PC, Supercomputer, Multi-platform, Workstation; Software requirements C and Fortan; Operation Systems/version is Linux/Unix or Windows« less

  16. Stochastic Inversion of 2D Magnetotelluric Data

    SciTech Connect

    Chen, Jinsong

    2010-07-01

    The algorithm is developed to invert 2D magnetotelluric (MT) data based on sharp boundary parametrization using a Bayesian framework. Within the algorithm, we consider the locations and the resistivity of regions formed by the interfaces are as unknowns. We use a parallel, adaptive finite-element algorithm to forward simulate frequency-domain MT responses of 2D conductivity structure. Those unknown parameters are spatially correlated and are described by a geostatistical model. The joint posterior probability distribution function is explored by Markov Chain Monte Carlo (MCMC) sampling methods. The developed stochastic model is effective for estimating the interface locations and resistivity. Most importantly, it provides details uncertainty information on each unknown parameter. Hardware requirements: PC, Supercomputer, Multi-platform, Workstation; Software requirements C and Fortan; Operation Systems/version is Linux/Unix or Windows

  17. Explicit 2-D Hydrodynamic FEM Program

    1996-08-07

    DYNA2D* is a vectorized, explicit, two-dimensional, axisymmetric and plane strain finite element program for analyzing the large deformation dynamic and hydrodynamic response of inelastic solids. DYNA2D* contains 13 material models and 9 equations of state (EOS) to cover a wide range of material behavior. The material models implemented in all machine versions are: elastic, orthotropic elastic, kinematic/isotropic elastic plasticity, thermoelastoplastic, soil and crushable foam, linear viscoelastic, rubber, high explosive burn, isotropic elastic-plastic, temperature-dependent elastic-plastic. Themore » isotropic and temperature-dependent elastic-plastic models determine only the deviatoric stresses. Pressure is determined by one of 9 equations of state including linear polynomial, JWL high explosive, Sack Tuesday high explosive, Gruneisen, ratio of polynomials, linear polynomial with energy deposition, ignition and growth of reaction in HE, tabulated compaction, and tabulated.« less

  18. Schottky diodes from 2D germanane

    NASA Astrophysics Data System (ADS)

    Sahoo, Nanda Gopal; Esteves, Richard J.; Punetha, Vinay Deep; Pestov, Dmitry; Arachchige, Indika U.; McLeskey, James T.

    2016-07-01

    We report on the fabrication and characterization of a Schottky diode made using 2D germanane (hydrogenated germanene). When compared to germanium, the 2D structure has higher electron mobility, an optimal band-gap, and exceptional stability making germanane an outstanding candidate for a variety of opto-electronic devices. One-atom-thick sheets of hydrogenated puckered germanium atoms have been synthesized from a CaGe2 framework via intercalation and characterized by XRD, Raman, and FTIR techniques. The material was then used to fabricate Schottky diodes by suspending the germanane in benzonitrile and drop-casting it onto interdigitated metal electrodes. The devices demonstrate significant rectifying behavior and the outstanding potential of this material.

  19. Layer Engineering of 2D Semiconductor Junctions.

    PubMed

    He, Yongmin; Sobhani, Ali; Lei, Sidong; Zhang, Zhuhua; Gong, Yongji; Jin, Zehua; Zhou, Wu; Yang, Yingchao; Zhang, Yuan; Wang, Xifan; Yakobson, Boris; Vajtai, Robert; Halas, Naomi J; Li, Bo; Xie, Erqing; Ajayan, Pulickel

    2016-07-01

    A new concept for junction fabrication by connecting multiple regions with varying layer thicknesses, based on the thickness dependence, is demonstrated. This type of junction is only possible in super-thin-layered 2D materials, and exhibits similar characteristics as p-n junctions. Rectification and photovoltaic effects are observed in chemically homogeneous MoSe2 junctions between domains of different thicknesses. PMID:27136275

  20. 2dF mechanical engineering

    NASA Astrophysics Data System (ADS)

    Smith, Greg; Lankshear, Allan

    1998-07-01

    2dF is a multi-object instrument mounted at prime focus at the AAT capable of spectroscopic analysis of 400 objects in a single 2 degree field. It also prepares a second 2 degree 400 object field while the first field is being observed. At its heart is a high precision robotic positioner that places individual fiber end magnetic buttons on one of two field plates. The button gripper is carried on orthogonal gantries powered by linear synchronous motors and contains a TV camera which precisely locates backlit buttons to allow placement in user defined locations to 10 (mu) accuracy. Fiducial points on both plates can also be observed by the camera to allow repeated checks on positioning accuracy. Field plates rotate to follow apparent sky rotation. The spectrographs both analyze light from the 200 observing fibers each and back- illuminate the 400 fibers being re-positioned during the observing run. The 2dF fiber position and spectrograph system is a large and complex instrument located at the prime focus of the Anglo Australian Telescope. The mechanical design has departed somewhat from the earlier concepts of Gray et al, but still reflects the audacity of those first ideas. The positioner is capable of positioning 400 fibers on a field plate while another 400 fibers on another plate are observing at the focus of the telescope and feeding the twin spectrographs. When first proposed it must have seemed like ingenuity unfettered by caution. Yet now it works, and works wonderfully well. 2dF is a system which functions as the result of the combined and coordinated efforts of the astronomers, the mechanical designers and tradespeople, the electronic designers, the programmers, the support staff at the telescope, and the manufacturing subcontractors. The mechanical design of the 2dF positioner and spectrographs was carried out by the mechanical engineering staff of the AAO and the majority of the manufacture was carried out in the AAO workshops.

  1. Realistic and efficient 2D crack simulation

    NASA Astrophysics Data System (ADS)

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

    Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.

  2. Compact 2-D graphical representation of DNA

    NASA Astrophysics Data System (ADS)

    Randić, Milan; Vračko, Marjan; Zupan, Jure; Novič, Marjana

    2003-05-01

    We present a novel 2-D graphical representation for DNA sequences which has an important advantage over the existing graphical representations of DNA in being very compact. It is based on: (1) use of binary labels for the four nucleic acid bases, and (2) use of the 'worm' curve as template on which binary codes are placed. The approach is illustrated on DNA sequences of the first exon of human β-globin and gorilla β-globin.

  3. 2D materials: Graphene and others

    NASA Astrophysics Data System (ADS)

    Bansal, Suneev Anil; Singh, Amrinder Pal; Kumar, Suresh

    2016-05-01

    Present report reviews the recent advancements in new atomically thick 2D materials. Materials covered in this review are Graphene, Silicene, Germanene, Boron Nitride (BN) and Transition metal chalcogenides (TMC). These materials show extraordinary mechanical, electronic and optical properties which make them suitable candidates for future applications. Apart from unique properties, tune-ability of highly desirable properties of these materials is also an important area to be emphasized on.

  4. TACO (2D AND 3D). Taco

    SciTech Connect

    Mason, W.E.

    1983-03-01

    A set of finite element codes for the solution of nonlinear, two-dimensional (TACO2D) and three-dimensional (TACO3D) heat transfer problems. Performs linear and nonlinear analyses of both transient and steady state heat transfer problems. Has the capability to handle time or temperature dependent material properties. Materials may be either isotropic or orthotropic. A variety of time and temperature dependent boundary conditions and loadings are available including temperature, flux, convection, radiation, and internal heat generation.

  5. Tomosynthesis imaging with 2D scanning trajectories

    NASA Astrophysics Data System (ADS)

    Khare, Kedar; Claus, Bernhard E. H.; Eberhard, Jeffrey W.

    2011-03-01

    Tomosynthesis imaging in chest radiography provides volumetric information with the potential for improved diagnostic value when compared to the standard AP or LAT projections. In this paper we explore the image quality benefits of 2D scanning trajectories when coupled with advanced image reconstruction approaches. It is intuitively clear that 2D trajectories provide projection data that is more complete in terms of Radon space filling, when compared with conventional tomosynthesis using a linearly scanned source. Incorporating this additional information for obtaining improved image quality is, however, not a straightforward problem. The typical tomosynthesis reconstruction algorithms are based on direct inversion methods e.g. Filtered Backprojection (FBP) or iterative algorithms that are variants of the Algebraic Reconstruction Technique (ART). The FBP approach is fast and provides high frequency details in the image but at the same time introduces streaking artifacts degrading the image quality. The iterative methods can reduce the image artifacts by using image priors but suffer from a slow convergence rate, thereby producing images lacking high frequency details. In this paper we propose using a fast converging optimal gradient iterative scheme that has advantages of both the FBP and iterative methods in that it produces images with high frequency details while reducing the image artifacts. We show that using favorable 2D scanning trajectories along with the proposed reconstruction method has the advantage of providing improved depth information for structures such as the spine and potentially producing images with more isotropic resolution.

  6. MAGNUM-2D computer code: user's guide

    SciTech Connect

    England, R.L.; Kline, N.W.; Ekblad, K.J.; Baca, R.G.

    1985-01-01

    Information relevant to the general use of the MAGNUM-2D computer code is presented. This computer code was developed for the purpose of modeling (i.e., simulating) the thermal and hydraulic conditions in the vicinity of a waste package emplaced in a deep geologic repository. The MAGNUM-2D computer computes (1) the temperature field surrounding the waste package as a function of the heat generation rate of the nuclear waste and thermal properties of the basalt and (2) the hydraulic head distribution and associated groundwater flow fields as a function of the temperature gradients and hydraulic properties of the basalt. MAGNUM-2D is a two-dimensional numerical model for transient or steady-state analysis of coupled heat transfer and groundwater flow in a fractured porous medium. The governing equations consist of a set of coupled, quasi-linear partial differential equations that are solved using a Galerkin finite-element technique. A Newton-Raphson algorithm is embedded in the Galerkin functional to formulate the problem in terms of the incremental changes in the dependent variables. Both triangular and quadrilateral finite elements are used to represent the continuum portions of the spatial domain. Line elements may be used to represent discrete conduits. 18 refs., 4 figs., 1 tab.

  7. Engineering light outcoupling in 2D materials.

    PubMed

    Lien, Der-Hsien; Kang, Jeong Seuk; Amani, Matin; Chen, Kevin; Tosun, Mahmut; Wang, Hsin-Ping; Roy, Tania; Eggleston, Michael S; Wu, Ming C; Dubey, Madan; Lee, Si-Chen; He, Jr-Hau; Javey, Ali

    2015-02-11

    When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs and solar cells. PMID:25602462

  8. An improved mechanically durable electrophoresis gel matrix that is fully compatible with fluorescence-based protein detection technologies.

    PubMed

    Schulenberg, Birte; Arnold, Brad; Patton, Wayne F

    2003-07-01

    Unfortunately, conventional large-format polyacrylamide gels are mechanically fragile, often tearing during the subsequent manipulations required for visualization of the proteins. This problem is compounded when large-format two-dimensional gels are subjected to multiple staining procedures in order to detect different classes of proteins, such as total protein, phosphoproteins, and glycoproteins. A mechanically durable liquid polyacrylamide-based matrix has been developed that, upon polymerization, facilitates the handling of one-dimensional and two-dimensional gels. The matrix, referred to as Rhinohide liquid acrylamide, is stable as a refrigerated solution for up to one year, and forms a polymer-reinforced polyacrylamide gel suitable for electrophoresis, upon addition of catalysts. The matrix is superior to previously reported durable gel matrices in that it does not cause distortion of high-molecular-weight bands and does not suffer from other spot morphology artifacts, such as doubling of protein spots in the molecular weight dimension. The matrix is particularly valuable for the analysis of proteins applying multiple applications of fluorescent dyes, as required with serial staining of proteins for phosphorylation, glycosylation, and total protein expression, using Pro-Q Diamond phosphoprotein stain, Pro-Q Emerald glycoprotein stain and SYPRO Ruby protein gel stain, respectively. PMID:12872220

  9. 2D superconductivity by ionic gating

    NASA Astrophysics Data System (ADS)

    Iwasa, Yoshi

    2D superconductivity is attracting a renewed interest due to the discoveries of new highly crystalline 2D superconductors in the past decade. Superconductivity at the oxide interfaces triggered by LaAlO3/SrTiO3 has become one of the promising routes for creation of new 2D superconductors. Also, the MBE grown metallic monolayers including FeSe are also offering a new platform of 2D superconductors. In the last two years, there appear a variety of monolayer/bilayer superconductors fabricated by CVD or mechanical exfoliation. Among these, electric field induced superconductivity by electric double layer transistor (EDLT) is a unique platform of 2D superconductivity, because of its ability of high density charge accumulation, and also because of the versatility in terms of materials, stemming from oxides to organics and layered chalcogenides. In this presentation, the following issues of electric filed induced superconductivity will be addressed; (1) Tunable carrier density, (2) Weak pinning, (3) Absence of inversion symmetry. (1) Since the sheet carrier density is quasi-continuously tunable from 0 to the order of 1014 cm-2, one is able to establish an electronic phase diagram of superconductivity, which will be compared with that of bulk superconductors. (2) The thickness of superconductivity can be estimated as 2 - 10 nm, dependent on materials, and is much smaller than the in-plane coherence length. Such a thin but low resistance at normal state results in extremely weak pinning beyond the dirty Boson model in the amorphous metallic films. (3) Due to the electric filed, the inversion symmetry is inherently broken in EDLT. This feature appears in the enhancement of Pauli limit of the upper critical field for the in-plane magnetic fields. In transition metal dichalcogenide with a substantial spin-orbit interactions, we were able to confirm the stabilization of Cooper pair due to its spin-valley locking. This work has been supported by Grant-in-Aid for Specially

  10. Low-cost two-dimensional gel densitometry

    SciTech Connect

    Levenson, R.M.; Maytin, E.V.; Young, D.A.

    1986-11-01

    A major obstacle to full utilization of the powerful technique of two-dimensional (2-D) gel electrophoresis is the expense and complexity of quantifying the results. Using an analog-to-digital converter already present in the widely available Commodore 64 or Commodore 128 microcomputer, the authors have developed a 2-D gel densitometer (GELSCAN) which adds only $20.00 to the cost of the Commodore system (currently around $700.00). The system is designed to work with autoradiograms of 2-D gels. Spots of interest are identified visually and then positioned manually over a light source. A pinhole photoelectric sensor mounted in a hand-held, Plexiglas holder, or mouse, is briefly rubbed over each spot. Maximum density of the spot is determined and its value is converted to counts per minute via an internal calibration curve which corrects for the nonlinear response of film to radiation. Local spot backgrounds can be subtracted and values can be normalized between gels to adjust for variation in amount of radioactivity applied or in exposure time. Reproducibility is excellent and the technique has some practical as well as theoretical advantages over other more complicated approaches to 2-D gel densitometry. In addition, the GELSCAN system can also be used for scanning individual bands in 1-D gels, quantitation of dot-blot autoradiograms and other tasks involving transmission densitometry.

  11. Chemical gel barriers as low-cost alternative to containment and in situ cleanup of hazardous wastes to protect groundwater

    SciTech Connect

    1997-01-01

    Chemical gel barriers are being considered as a low-cost alternative for containment and in situ cleanup of hazardous wastes to protect groundwater. Most of the available gels in petroleum application are non-reactive and relative impermeable, providing a physical barriers for all fluids and contaminants. However, other potential systems can be envisioned. These systems could include gels that are chemically reactive and impermeable such that most phase are captured by the barriers but the contaminants could diffuse through the barriers. Another system that is chemically reactive and permeable could have potential applications in selectivity capturing contaminants while allowing water to pass through the barriers. This study focused on chemically reactive and permeable gel barriers. The gels used in experiment are DuPont LUDOX SM colloidal silica gel and Pfizer FLOPAAM 1330S hydrolyzed polyacrylamide (HPAM) gel.

  12. How deeply cells feel: methods for thin gels

    NASA Astrophysics Data System (ADS)

    Buxboim, Amnon; Rajagopal, Karthikan; Brown, Andre'E. X.; Discher, Dennis E.

    2010-05-01

    Tissue cells lack the ability to see or hear but have evolved mechanisms to feel into their surroundings and sense a collective stiffness. A cell can even sense the effective stiffness of rigid objects that are not in direct cellular contact—like the proverbial princess who feels a pea placed beneath soft mattresses. How deeply a cell feels into a matrix can be measured by assessing cell responses on a controlled series of thin and elastic gels that are affixed to a rigid substrate. Gel elasticity E is readily varied with polymer concentrations of now-standard polyacrylamide hydrogels, but to eliminate wrinkling and detachment of thin gels from an underlying glass coverslip, vinyl groups are bonded to the glass before polymerization. Gel thickness is nominally specified using micron-scale beads that act as spacers, but gels swell after polymerization as measured by z-section, confocal microscopy of fluorescent gels. Atomic force microscopy is used to measure E at gel surfaces, employing stresses and strains that are typically generated by cells and yielding values for E that span a broad range of tissue microenvironments. To illustrate cell sensitivities to a series of thin-to-thick gels, the adhesive spreading of mesenchymal stem cells was measured on gel mimics of a very soft tissue (e.g. brain, E ~ 1 kPa). Initial results show that cells increasingly respond to the rigidity of an underlying 'hidden' surface starting at about 10-20 µm gel thickness with a characteristic tactile length of less than about 5 µm.

  13. Electric Field Enhanced Diffusion of Salicylic Acid through Polyacrylamide Hydrogels

    NASA Astrophysics Data System (ADS)

    Niamlang, Sumonman; Sirivat, Anuvat

    2008-03-01

    The release mechanisms and the diffusion coefficients of salicylic acid -loaded polyacrylamide hydrogels were investigated experimentally by using a modified Franz-diffusion cell at 37 ^oC to determine the effects of crosslinking ratio and electric field strength. A significant amount of salicylic acid is released within 48 hours from the hydrogels of various crosslinking ratios, with and without electric field. The release characteristic follows the Q vs. t^1/2 linear relationship. Diffusion coefficient initially increases with increasing electric field strength and reaches the maximum value at electric field strength of 0.1 V; beyond that it decreases with electric field strength and becomes saturated at electric field strength of 5 V. The diffusion coefficient increases at low electric field strength (less 0.1 V) as a result of the electrophoresis of the salicylic acid, the expansion of pore size, and the induced pathway in pigskin. For electric field strength higher than 0.1 V, the decrease in the diffusion coefficient is due to the reduction of the polyacrylamide pore size. The diffusion coefficient obeys the scaling behavior D/Do=(drug size/pore size)^m, with the scaling exponent m equal to 0.93 and 0.42 at electric fields of 0 and 0.1 V, respectively.

  14. 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.

  15. GBL-2D Version 1.0: a 2D geometry boolean library.

    SciTech Connect

    McBride, Cory L. (Elemental Technologies, American Fort, UT); Schmidt, Rodney Cannon; Yarberry, Victor R.; Meyers, Ray J.

    2006-11-01

    This report describes version 1.0 of GBL-2D, a geometric Boolean library for 2D objects. The library is written in C++ and consists of a set of classes and routines. The classes primarily represent geometric data and relationships. Classes are provided for 2D points, lines, arcs, edge uses, loops, surfaces and mask sets. The routines contain algorithms for geometric Boolean operations and utility functions. Routines are provided that incorporate the Boolean operations: Union(OR), XOR, Intersection and Difference. A variety of additional analytical geometry routines and routines for importing and exporting the data in various file formats are also provided. The GBL-2D library was originally developed as a geometric modeling engine for use with a separate software tool, called SummitView [1], that manipulates the 2D mask sets created by designers of Micro-Electro-Mechanical Systems (MEMS). However, many other practical applications for this type of software can be envisioned because the need to perform 2D Boolean operations can arise in many contexts.

  16. Interparticle Attraction in 2D Complex Plasmas

    NASA Astrophysics Data System (ADS)

    Kompaneets, Roman; Morfill, Gregor E.; Ivlev, Alexei V.

    2016-03-01

    Complex (dusty) plasmas allow experimental studies of various physical processes occurring in classical liquids and solids by directly observing individual microparticles. A major problem is that the interaction between microparticles is generally not molecularlike. In this Letter, we propose how to achieve a molecularlike interaction potential in laboratory 2D complex plasmas. We argue that this principal aim can be achieved by using relatively small microparticles and properly adjusting discharge parameters. If experimentally confirmed, this will make it possible to employ complex plasmas as a model system with an interaction potential resembling that of conventional liquids.

  17. Periodically sheared 2D Yukawa systems

    SciTech Connect

    Kovács, Anikó Zsuzsa; Hartmann, Peter; Donkó, Zoltán

    2015-10-15

    We present non-equilibrium molecular dynamics simulation studies on the dynamic (complex) shear viscosity of a 2D Yukawa system. We have identified a non-monotonic frequency dependence of the viscosity at high frequencies and shear rates, an energy absorption maximum (local resonance) at the Einstein frequency of the system at medium shear rates, an enhanced collective wave activity, when the excitation is near the plateau frequency of the longitudinal wave dispersion, and the emergence of significant configurational anisotropy at small frequencies and high shear rates.

  18. ENERGY LANDSCAPE OF 2D FLUID FORMS

    SciTech Connect

    Y. JIANG; ET AL

    2000-04-01

    The equilibrium states of 2D non-coarsening fluid foams, which consist of bubbles with fixed areas, correspond to local minima of the total perimeter. (1) The authors find an approximate value of the global minimum, and determine directly from an image how far a foam is from its ground state. (2) For (small) area disorder, small bubbles tend to sort inwards and large bubbles outwards. (3) Topological charges of the same sign repel while charges of opposite sign attract. (4) They discuss boundary conditions and the uniqueness of the pattern for fixed topology.

  19. A scalable 2-D parallel sparse solver

    SciTech Connect

    Kothari, S.C.; Mitra, S.

    1995-12-01

    Scalability beyond a small number of processors, typically 32 or less, is known to be a problem for existing parallel general sparse (PGS) direct solvers. This paper presents a parallel general sparse PGS direct solver for general sparse linear systems on distributed memory machines. The algorithm is based on the well-known sequential sparse algorithm Y12M. To achieve efficient parallelization, a 2-D scattered decomposition of the sparse matrix is used. The proposed algorithm is more scalable than existing parallel sparse direct solvers. Its scalability is evaluated on a 256 processor nCUBE2s machine using Boeing/Harwell benchmark matrices.

  20. 2D stepping drive for hyperspectral systems

    NASA Astrophysics Data System (ADS)

    Endrödy, Csaba; Mehner, Hannes; Grewe, Adrian; Sinzinger, Stefan; Hoffmann, Martin

    2015-07-01

    We present the design, fabrication and characterization of a compact 2D stepping microdrive for pinhole array positioning. The miniaturized solution enables a highly integrated compact hyperspectral imaging system. Based on the geometry of the pinhole array, an inch-worm drive with electrostatic actuators was designed resulting in a compact (1 cm2) positioning system featuring a step size of about 15 µm in a 170 µm displacement range. The high payload (20 mg) as required for the pinhole array and the compact system design exceed the known electrostatic inch-worm-based microdrives.

  1. Low-velocity super-lubrication of sodium-alginate/polyacrylamide ionic-covalent hybrid double-network hydrogels.

    PubMed

    Li, Xuefeng; Wu, Chu; Yang, Qian; Long, Shijun; Wu, Chonggang

    2015-04-21

    Structural and frictional behaviours of sodium alginate (SA)/polyacrylamide (PAAm) ionic-covalent hybrid, sequential double-network (DN) hydrogels against glass have been investigated in water, NaCl and CaCl2 aqueous solutions using a rotational rheometer. Dilution of adsorptive elastohydrodynamic friction for the PAAm covalent network with repulsive hydrodynamic lubrication for the minor SA ionic network was found to control the frictional stresses of the SA/PAAm gels within between those of the SA and PAAm single-network gels. A tentative qualitative model was proposed to describe the impact of ionic environmental solution on the frictional behaviour of the hybrid gel by selectively affecting the SA-network structure and friction. It was revealed that strong Debye shielding in the NaCl solution significantly reduced the thickness of the electric double layer for hydrodynamic lubrication of the SA network, which made the SA/PAAm gel's friction the highest among the three solutions. Dramatically increased ionic cross-linking of the SA network in the CaCl2 solution, although effectively mediated by the PAAm-network flexible skeleton, still functioned partially to conserve a portion of the SA fractional boundary-friction at the interface, making the friction of the hybrid gel intermediate among the three solutions. In contrast, extreme hydration of the SA network in water sharply increased the volume fraction of its unshielded hydrodynamic lubrication at the interface, which greatly reduced the SA/PAAm's friction to the lowest among the three solutions. We have thus incorporated for the first time both super-lubrication (frictional coefficients of below 10(-2) over low sliding-velocities of 3 × 10(-5) to 2 × 10(-3) m s(-1)) and previously reported high fracture energy (over 9000 J m(-2)) into a single ionic-covalent hybrid DN hydrogel, which is the SA/PAAm (∼1/8.5 w/w) gel in water. Effects of inversion of DN-formation sequence further indicated that frictional

  2. Fundamentals of gel dosimeters

    NASA Astrophysics Data System (ADS)

    McAuley, K. B.; Nasr, A. T.

    2013-06-01

    Fundamental chemical and physical phenomena that occur in Fricke gel dosimeters, polymer gel dosimeters, micelle gel dosimeters and genipin gel dosimeters are discussed. Fricke gel dosimeters are effective even though their radiation sensitivity depends on oxygen concentration. Oxygen contamination can cause severe problems in polymer gel dosimeters, even when THPC is used. Oxygen leakage must be prevented between manufacturing and irradiation of polymer gels, and internal calibration methods should be used so that contamination problems can be detected. Micelle gel dosimeters are promising due to their favourable diffusion properties. The introduction of micelles to gel dosimetry may open up new areas of dosimetry research wherein a range of water-insoluble radiochromic materials can be explored as reporter molecules.

  3. Application of Bessel beams to 2D microfabrication

    NASA Astrophysics Data System (ADS)

    Li, X.-F.; Winfield, R. J.; O'Brien, S.; Crean, G. M.

    2009-03-01

    Fs laser-based two-photon polymerisation (2PP) has been widely reported as a means of directly writing three-dimensional nanoscale structures. Usually the voxel of a high numerical aperture microscope objective is scanned through the resin to build up the required model. In the case of high aspect ratio two-dimensional structures, such as cell scaffolds, repeated scanning is required to build up the height. The voxel shape can be substantially elongated by the inclusion of an axicon lens in the laser beam line. In this report we describe the use of a Bessel beam produced in the region beyond the focus of an objective lens when the beam has been modified in this way. A Ti:sapphire laser was used to write a range of 2D square cell structures in a Zr-loaded sol-gel system. The process was characterised, in terms of the dimensions of the polymerised Bessel region, for different processing conditions. Examples of the structures are also described.

  4. Human 2-D PAGE databases for proteome analysis in health and disease: http://biobase.dk/cgi-bin/celis.

    PubMed

    Celis, J E; Gromov, P; Ostergaard, M; Madsen, P; Honoré, B; Dejgaard, K; Olsen, E; Vorum, H; Kristensen, D B; Gromova, I; Haunsø, A; Van Damme, J; Puype, M; Vandekerckhove, J; Rasmussen, H H

    1996-12-01

    Human 2-D PAGE Databases established at the Danish Centre for Human Genome Research are now available on the World Wide Web (http://biobase.dk/cgi-bin/celis). The databanks, which offer a comprehensive approach to the analysis of the human proteome both in health and disease, contain data on known and unknown proteins recorded in various IEF and NEPHGE 2-D PAGE reference maps (non-cultured keratinocytes, non-cultured transitional cell carcinomas, MRC-5 fibroblasts and urine). One can display names and information on specific protein spots by clicking on the image of the gel representing the 2-D gel map in which one is interested. In addition, the database can be searched by protein name, keywords or organelle or cellular component. The entry files contain links to other databases such as Medline, Swiss-Prot, PIR, PDB, CySPID, OMIM, Methabolic pathways, etc. The on-line information is updated regularly. PMID:8977092

  5. WFR-2D: an analytical model for PWAS-generated 2D ultrasonic guided wave propagation

    NASA Astrophysics Data System (ADS)

    Shen, Yanfeng; Giurgiutiu, Victor

    2014-03-01

    This paper presents WaveFormRevealer 2-D (WFR-2D), an analytical predictive tool for the simulation of 2-D ultrasonic guided wave propagation and interaction with damage. The design of structural health monitoring (SHM) systems and self-aware smart structures requires the exploration of a wide range of parameters to achieve best detection and quantification of certain types of damage. Such need for parameter exploration on sensor dimension, location, guided wave characteristics (mode type, frequency, wavelength, etc.) can be best satisfied with analytical models which are fast and efficient. The analytical model was constructed based on the exact 2-D Lamb wave solution using Bessel and Hankel functions. Damage effects were inserted in the model by considering the damage as a secondary wave source with complex-valued directivity scattering coefficients containing both amplitude and phase information from wave-damage interaction. The analytical procedure was coded with MATLAB, and a predictive simulation tool called WaveFormRevealer 2-D was developed. The wave-damage interaction coefficients (WDICs) were extracted from harmonic analysis of local finite element model (FEM) with artificial non-reflective boundaries (NRB). The WFR-2D analytical simulation results were compared and verified with full scale multiphysics finite element models and experiments with scanning laser vibrometer. First, Lamb wave propagation in a pristine aluminum plate was simulated with WFR-2D, compared with finite element results, and verified by experiments. Then, an inhomogeneity was machined into the plate to represent damage. Analytical modeling was carried out, and verified by finite element simulation and experiments. This paper finishes with conclusions and suggestions for future work.

  6. Microwave Assisted 2D Materials Exfoliation

    NASA Astrophysics Data System (ADS)

    Wang, Yanbin

    Two-dimensional materials have emerged as extremely important materials with applications ranging from energy and environmental science to electronics and biology. Here we report our discovery of a universal, ultrafast, green, solvo-thermal technology for producing excellent-quality, few-layered nanosheets in liquid phase from well-known 2D materials such as such hexagonal boron nitride (h-BN), graphite, and MoS2. We start by mixing the uniform bulk-layered material with a common organic solvent that matches its surface energy to reduce the van der Waals attractive interactions between the layers; next, the solutions are heated in a commercial microwave oven to overcome the energy barrier between bulk and few-layers states. We discovered the minutes-long rapid exfoliation process is highly temperature dependent, which requires precise thermal management to obtain high-quality inks. We hypothesize a possible mechanism of this proposed solvo-thermal process; our theory confirms the basis of this novel technique for exfoliation of high-quality, layered 2D materials by using an as yet unknown role of the solvent.

  7. Photocurrent spectroscopy of 2D materials

    NASA Astrophysics Data System (ADS)

    Cobden, David

    Confocal photocurrent measurements provide a powerful means of studying many aspects of the optoelectronic and electrical properties of a 2D device or material. At a diffraction-limited point they can provide a detailed absorption spectrum, and they can probe local symmetry, ultrafast relaxation rates and processes, electron-electron interaction strengths, and transport coefficients. We illustrate this with several examples, once being the photo-Nernst effect. In gapless 2D materials, such as graphene, in a perpendicular magnetic field a photocurrent antisymmetric in the field is generated near to the free edges, with opposite sign at opposite edges. Its origin is the transverse thermoelectric current associated with the laser-induced electron temperature gradient. This effect provides an unambiguous demonstration of the Shockley-Ramo nature of long-range photocurrent generation in gapless materials. It also provides a means of investigating quasiparticle properties. For example, in the case of graphene on hBN, it can be used to probe the Lifshitz transition that occurs due to the minibands formed by the Moire superlattice. We also observe and discuss photocurrent generated in other semimetallic (WTe2) and semiconducting (WSe2) monolayers. Work supported by DoE BES and NSF EFRI grants.

  8. Multienzyme Inkjet Printed 2D Arrays.

    PubMed

    Gdor, Efrat; Shemesh, Shay; Magdassi, Shlomo; Mandler, Daniel

    2015-08-19

    The use of printing to produce 2D arrays is well established, and should be relatively facile to adapt for the purpose of printing biomaterials; however, very few studies have been published using enzyme solutions as inks. Among the printing technologies, inkjet printing is highly suitable for printing biomaterials and specifically enzymes, as it offers many advantages. Formulation of the inkjet inks is relatively simple and can be adjusted to a variety of biomaterials, while providing nonharmful environment to the enzymes. Here we demonstrate the applicability of inkjet printing for patterning multiple enzymes in a predefined array in a very straightforward, noncontact method. Specifically, various arrays of the enzymes glucose oxidase (GOx), invertase (INV) and horseradish peroxidase (HP) were printed on aminated glass surfaces, followed by immobilization using glutardialdehyde after printing. Scanning electrochemical microscopy (SECM) was used for imaging the printed patterns and to ascertain the enzyme activity. The successful formation of 2D arrays consisting of enzymes was explored as a means of developing the first surface confined enzyme based logic gates. Principally, XOR and AND gates, each consisting of two enzymes as the Boolean operators, were assembled, and their operation was studied by SECM. PMID:26214072

  9. 21 CFR 872.3480 - Polyacrylamide polymer (modified cationic) denture adhesive.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... adhesive. 872.3480 Section 872.3480 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND... polymer (modified cationic) denture adhesive. (a) Identification. A polyacrylamide polymer (modified cationic) denture adhesive is a device composed of polyacrylamide polymer (modified cationic) intended...

  10. 21 CFR 872.3480 - Polyacrylamide polymer (modified cationic) denture adhesive.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... adhesive. 872.3480 Section 872.3480 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND... polymer (modified cationic) denture adhesive. (a) Identification. A polyacrylamide polymer (modified cationic) denture adhesive is a device composed of polyacrylamide polymer (modified cationic) intended...

  11. 21 CFR 872.3480 - Polyacrylamide polymer (modified cationic) denture adhesive.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... adhesive. 872.3480 Section 872.3480 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND... polymer (modified cationic) denture adhesive. (a) Identification. A polyacrylamide polymer (modified cationic) denture adhesive is a device composed of polyacrylamide polymer (modified cationic) intended...

  12. 2-D or not 2-D, that is the question: A Northern California test

    SciTech Connect

    Mayeda, K; Malagnini, L; Phillips, W S; Walter, W R; Dreger, D

    2005-06-06

    Reliable estimates of the seismic source spectrum are necessary for accurate magnitude, yield, and energy estimation. In particular, how seismic radiated energy scales with increasing earthquake size has been the focus of recent debate within the community and has direct implications on earthquake source physics studies as well as hazard mitigation. The 1-D coda methodology of Mayeda et al. has provided the lowest variance estimate of the source spectrum when compared against traditional approaches that use direct S-waves, thus making it ideal for networks that have sparse station distribution. The 1-D coda methodology has been mostly confined to regions of approximately uniform complexity. For larger, more geophysically complicated regions, 2-D path corrections may be required. The complicated tectonics of the northern California region coupled with high quality broadband seismic data provides for an ideal ''apples-to-apples'' test of 1-D and 2-D path assumptions on direct waves and their coda. Using the same station and event distribution, we compared 1-D and 2-D path corrections and observed the following results: (1) 1-D coda results reduced the amplitude variance relative to direct S-waves by roughly a factor of 8 (800%); (2) Applying a 2-D correction to the coda resulted in up to 40% variance reduction from the 1-D coda results; (3) 2-D direct S-wave results, though better than 1-D direct waves, were significantly worse than the 1-D coda. We found that coda-based moment-rate source spectra derived from the 2-D approach were essentially identical to those from the 1-D approach for frequencies less than {approx}0.7-Hz, however for the high frequencies (0.7{le} f {le} 8.0-Hz), the 2-D approach resulted in inter-station scatter that was generally 10-30% smaller. For complex regions where data are plentiful, a 2-D approach can significantly improve upon the simple 1-D assumption. In regions where only 1-D coda correction is available it is still preferable over 2

  13. Polyacrylamide polymer viscosity as a function of brine composition

    SciTech Connect

    French, T.R.; Stacy, N.; Collins, A.G.

    1981-05-01

    A computer model has been developed which predicts the viscosity of polymer and oil field brine mixtures. The polymers used were Amoco- Sweepaid 103 and Dow- Pusher 500 polyacrylamide polymers. All of the experiments were conducted at 1200 ppM polymer concentration. The computer input consists of the ionic strength of the brine in the mixture and the fraction of that ionic strength due to sodium ions. The computer program makes predictions of viscosity by referencing a family of viscosity curves for various mixtures of sodium chloride and calcium chloride in 1200 ppM polymer solutions. The model has been tested using 59 mixtures of brines and polymers. The ionic strength of the brine in the mixtures varied from 0.0018 to 0.025. The fraction of the brines' total ionic strength due to sodium ions varied from 0.22 to 0.49. The brines consisted predominantly of sodium, potassium, magnesium, calcium, chloride, bicarbonate and sulfate ions.

  14. Treatment of complications from polyacrylamide hydrogel breast augmentation

    PubMed Central

    WEI, WANG

    2016-01-01

    Polyacrylamide hydrogel (PAHG) is a medical soft tissue filling agent utilized for the treatment of a variety of soft tissue defects. However, postoperative complications occur that have to be alleviated. The aim of the present study was to examine the treatments of postoperative complications of mammoplasty augmentation with PAHG. Open suction techniques and partial mastectomies via periareolar incisions were performed in 28 patients who had been injected with PAHG for breast augmentation. The PAHG was removed precluding breast complications resulting from the hydrogel injections. The symptoms disappeared completely, and the results were satisfactory following removal of the PAHG. In conclusion, the periareolar approach is valuable and removes PAHG to the greatest extent. PMID:27347035

  15. Hydrolyzed polyacrylamide biodegradation and mechanism in sequencing batch biofilm reactor.

    PubMed

    Yan, Miao; Zhao, Lanmei; Bao, Mutai; Lu, Jinren

    2016-05-01

    An investigation was performed to study the performance of a sequencing batch biofilm reactor (SBBR) to treat hydrolyzed polyacrylamides (HPAMs) and to determine the mechanisms of HPAM biodegradation. The mechanisms for the optimized parameters that significantly improved the degradation efficiency of the HPAMs were investigated by a synergistic effect of the co-metabolism in the sludge and the enzyme activities. The HPAM and TOC removal ratio reached 54.69% and 70.14%. A significant decrease in the total nitrogen concentration was measured. The carbon backbone of the HPAMs could be degraded after the separation of the amide group according to the data analysis. The HPLC results indicated that the HPAMs could be converted to polymer fragments without the generation of the acrylamide monomer intermediate. The results from high-throughput sequencing analysis revealed proteobacterias, bacteroidetes and planctomycetes were the key microorganisms involved in the degradation. PMID:26896716

  16. DEVELOPMENT OF POLYMER GEL SYSTEMS TO IMPROVE VOLUMETRIC SWEEP AND REDUCE PRODUCING WATER/OIL RATIOS

    SciTech Connect

    G. Paul Willhite; Stan McCool; Don W. Green; Min Cheng; Rajeev Jain; Tuan Nguyen

    2003-11-01

    Gelled polymer treatments are applied to oil reservoirs to increase oil production and to reduce water production by altering the fluid movement within the reservoir. This report describes the results of the first year of a three-year research program that is aimed at the understanding of the chemistry of gelation and the fundamental mechanisms that alter the flows of oil and water in reservoir rocks after a gel treatment. Work has focused on a widely-applied system in field applications, the partially hydrolyzed polyacrylamide-chromium acetate gel. Gelation occurs by network formation through the crosslinking of polyacrylamide molecules as a result of reaction with chromium acetate. The initial reaction between chromium acetate and one polymer is referred to as the uptake reaction. The uptake reaction was studied as functions of chromium and polymer concentrations and pH values. Experimental data were regressed to determine a rate equation that describes the uptake reaction of chromium by polyacrylamide. Pre-gel aggregates form and grow as the reactions between chromium acetate and polyacrylamide proceed. A statistical model that describes the growth of pre-gel aggregates was developed using the theory of branching processes. The model gives molecular weight averages that are expressed as functions of the conversion of the reactive sites on chromium acetate or on the polymer molecule. Results of the application of the model correlate well with experimental data of viscosity and weight-average molecular weight and gives insights into the gelation process. A third study addresses the flow of water and oil in rock material after a gel treatment. Previous works have shown that gel treatments usually reduce the permeability to water to a greater extent than the permeability to oil is reduced. This phenomenon is referred to as disproportionate permeability reduction (DPR). Flow experiments were conducted to determine the effect of polymer and chromium concentrations on

  17. Numerical Evaluation of 2D Ground States

    NASA Astrophysics Data System (ADS)

    Kolkovska, Natalia

    2016-02-01

    A ground state is defined as the positive radial solution of the multidimensional nonlinear problem \\varepsilon propto k_ bot 1 - ξ with the function f being either f(u) =a|u|p-1u or f(u) =a|u|pu+b|u|2pu. The numerical evaluation of ground states is based on the shooting method applied to an equivalent dynamical system. A combination of fourth order Runge-Kutta method and Hermite extrapolation formula is applied to solving the resulting initial value problem. The efficiency of this procedure is demonstrated in the 1D case, where the maximal difference between the exact and numerical solution is ≈ 10-11 for a discretization step 0:00025. As a major application, we evaluate numerically the critical energy constant. This constant is defined as a functional of the ground state and is used in the study of the 2D Boussinesq equations.

  18. Canard configured aircraft with 2-D nozzle

    NASA Technical Reports Server (NTRS)

    Child, R. D.; Henderson, W. P.

    1978-01-01

    A closely-coupled canard fighter with vectorable two-dimensional nozzle was designed for enhanced transonic maneuvering. The HiMAT maneuver goal of a sustained 8g turn at a free-stream Mach number of 0.9 and 30,000 feet was the primary design consideration. The aerodynamic design process was initiated with a linear theory optimization minimizing the zero percent suction drag including jet effects and refined with three-dimensional nonlinear potential flow techniques. Allowances were made for mutual interference and viscous effects. The design process to arrive at the resultant configuration is described, and the design of a powered 2-D nozzle model to be tested in the LRC 16-foot Propulsion Wind Tunnel is shown.

  19. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

    Burns, Devin E.; Oh, Lance H.; Li, Mary J.; Jones, Justin S.; Kelly, Daniel P.; Zheng, Yun; Kutyrev, Alexander S.; Moseley, Samuel H.

    2015-01-01

    An electrostatically actuated microshutter array consisting of rotational microshutters (shutters that rotate about a torsion bar) were designed and fabricated through the use of models and experiments. Design iterations focused on minimizing the torsional stiffness of the microshutters, while maintaining their structural integrity. Mechanical and electromechanical test systems were constructed to measure the static and dynamic behavior of the microshutters. The torsional stiffness was reduced by a factor of four over initial designs without sacrificing durability. Analysis of the resonant behavior of the microshutter arrays demonstrates that the first resonant mode is a torsional mode occurring around 3000 Hz. At low vacuum pressures, this resonant mode can be used to significantly reduce the drive voltage necessary for actuation requiring as little as 25V. 2D electrostatic latching and addressing was demonstrated using both a resonant and pulsed addressing scheme.

  20. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

    Burns, Devin E.; Oh, Lance H.; Li, Mary J.; Kelly, Daniel P.; Kutyrev, Alexander S.; Moseley, Samuel H.

    2015-01-01

    Electrostatically actuated microshutter arrays consisting of rotational microshutters (shutters that rotate about a torsion bar) were designed and fabricated through the use of models and experiments. Design iterations focused on minimizing the torsional stiffness of the microshutters, while maintaining their structural integrity. Mechanical and electromechanical test systems were constructed to measure the static and dynamic behavior of the microshutters. The torsional stiffness was reduced by a factor of four over initial designs without sacrificing durability. Analysis of the resonant behavior of the microshutters demonstrates that the first resonant mode is a torsional mode occurring around 3000 Hz. At low vacuum pressures, this resonant mode can be used to significantly reduce the drive voltage necessary for actuation requiring as little as 25V. 2D electrostatic latching and addressing was demonstrated using both a resonant and pulsed addressing scheme.

  1. Graphene suspensions for 2D printing

    NASA Astrophysics Data System (ADS)

    Soots, R. A.; Yakimchuk, E. A.; Nebogatikova, N. A.; Kotin, I. A.; Antonova, I. V.

    2016-04-01

    It is shown that, by processing a graphite suspension in ethanol or water by ultrasound and centrifuging, it is possible to obtain particles with thicknesses within 1-6 nm and, in the most interesting cases, 1-1.5 nm. Analogous treatment of a graphite suspension in organic solvent yields eventually thicker particles (up to 6-10 nm thick) even upon long-term treatment. Using the proposed ink based on graphene and aqueous ethanol with ethylcellulose and terpineol additives for 2D printing, thin (~5 nm thick) films with sheet resistance upon annealing ~30 MΩ/□ were obtained. With the ink based on aqueous graphene suspension, the sheet resistance was ~5-12 kΩ/□ for 6- to 15-nm-thick layers with a carrier mobility of ~30-50 cm2/(V s).

  2. Testosterone Nasal Gel

    MedlinePlus

    Testosterone nasal gel is used to treat symptoms of low testosterone in men who have hypogonadism (a condition in which the body does not produce enough natural testosterone). Testosterone nasal gel is used only for men ...

  3. 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.

  4. Metrology for graphene and 2D materials

    NASA Astrophysics Data System (ADS)

    Pollard, Andrew J.

    2016-09-01

    The application of graphene, a one atom-thick honeycomb lattice of carbon atoms with superlative properties, such as electrical conductivity, thermal conductivity and strength, has already shown that it can be used to benefit metrology itself as a new quantum standard for resistance. However, there are many application areas where graphene and other 2D materials, such as molybdenum disulphide (MoS2) and hexagonal boron nitride (h-BN), may be disruptive, areas such as flexible electronics, nanocomposites, sensing and energy storage. Applying metrology to the area of graphene is now critical to enable the new, emerging global graphene commercial world and bridge the gap between academia and industry. Measurement capabilities and expertise in a wide range of scientific areas are required to address this challenge. The combined and complementary approach of varied characterisation methods for structural, chemical, electrical and other properties, will allow the real-world issues of commercialising graphene and other 2D materials to be addressed. Here, examples of metrology challenges that have been overcome through a multi-technique or new approach are discussed. Firstly, the structural characterisation of defects in both graphene and MoS2 via Raman spectroscopy is described, and how nanoscale mapping of vacancy defects in graphene is also possible using tip-enhanced Raman spectroscopy (TERS). Furthermore, the chemical characterisation and removal of polymer residue on chemical vapour deposition (CVD) grown graphene via secondary ion mass spectrometry (SIMS) is detailed, as well as the chemical characterisation of iron films used to grow large domain single-layer h-BN through CVD growth, revealing how contamination of the substrate itself plays a role in the resulting h-BN layer. In addition, the role of international standardisation in this area is described, outlining the current work ongoing in both the International Organization of Standardization (ISO) and the

  5. The mouse ruby-eye 2(d) (ru2(d) /Hps5(ru2-d) ) allele inhibits eumelanin but not pheomelanin synthesis.

    PubMed

    Hirobe, Tomohisa; Ito, Shosuke; Wakamatsu, Kazumasa

    2013-09-01

    The novel mutation named ru2(d) /Hps5(ru2-d) , characterized by light-colored coats and ruby-eyes, prohibits differentiation of melanocytes by inhibiting tyrosinase (Tyr) activity, expression of Tyr, Tyr-related protein 1 (Tyrp1), Tyrp2, and Kit. However, it is not known whether the ru2(d) allele affects pheomelanin synthesis in recessive yellow (e/Mc1r(e) ) or in pheomelanic stage in agouti (A) mice. In this study, effects of the ru2(d) allele on pheomelanin synthesis were investigated by chemical analysis of melanin present in dorsal hairs of 5-week-old mice from F2 generation between C57BL/10JHir (B10)-co-isogenic ruby-eye 2(d) and B10-congenic recessive yellow or agouti. Eumelanin content was decreased in ruby-eye 2(d) and ruby-eye 2(d) agouti mice, whereas pheomelanin content in ruby-eye 2(d) recessive yellow and ruby-eye 2(d) agouti mice did not differ from the corresponding Ru2(d) /- mice, suggesting that the ru2(d) allele inhibits eumelanin but not pheomelanin synthesis. PMID:23672590

  6. 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.

  7. 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.

  8. Gel image segmentation based on discontinuity and region information

    NASA Astrophysics Data System (ADS)

    Wang, Weixing

    2005-10-01

    2-D electrophoresis gel images can be used for identifying and characterizing many forms of a particular protein encoded by a single gene. Conventional approaches to gel analysis require the three steps: (1) Spot detection on each gel; (2) Spot matching between gels; and (3) Spot quantification and comparison. Many researchers and developers attempt to automate all steps as much as possible, but errors in the detection and matching stages are common. In order to carry out gel image analysis, one first needs to accurately detect and measure the protein spots in a gel image. As other image analysis or computer vision areas, image segmentation is still a hard problem. This paper presents algorithms for automatically delineating gel spots. Two types of segmentation algorithms were implemented, the one is edge (discontinuity) based type, and the other is region based type. For the different classes of gel images, the two types of algorithms were tested; the advantages and disadvantages were discussed. Based on the testing and analysis results, authors suggested using a fusion of edge information and region information for gel image segmentation is a good complementary. The primary integration of the two types of image segmentation algorithms have been tested too, the result clearly show that the integrated algorithm can automatically delineate gel not only on a simple image and also on a complex image, and it is much better than that either only edge based algorithm or only region based algorithm.

  9. Cytotoxicity and altered c-myc gene expression by medical polyacrylamide hydrogel.

    PubMed

    Xi, T F; Fan, C X; Feng, X M; Wan, Z Y; Wang, C R; Chou, L L

    2006-08-01

    Medical Polyacrylamide Hydrogel (PAMG)has been used in plastic and aesthetic surgery for years. However, its safety is still in doubt in many countries. In the current research, first an approach, using high performance liquid chromatography (HPLC), to determine the amount of residual acrylamide monomer (AM) in the PAMG was presented. Then the cytotoxicity of PAMG was investigated using cell counting and methyl thiazolyl tetrazolium (MTT) assay. To explore the mechanism of this toxicity, normal human fibroblasts cultured in medium extracts were analyzed. Membrane changes and other related parameters were investigated using flow cytometry (FCM). Real time fluorescent polymerase chain reaction (real time PCR) was also introduced to determine the biological response of the fibroblasts. During this process, three representative genes (p53, beta-actin, and c-myc, which are tumor suppressor genes, housekeeping genes, and proto-oncogenes respectively) were selected for examination. Results indicated that a method based on HPLC is practical and simple for determining AM in PAMG. The detection limits can reach the desired ppb level, and so it can fully meet the requirements of the studies of PAMG. Polyacylamide Hydrogel inhibits the growth of human fibroblasts and may cause the apoptosis of human fibroblasts. Moreover, it can alter physical parameters such as the size and the granularity of these cells. Furthermore, these three genes have a relatively typical amplification plot and highly related, wide-range standard curves, and so this reaction system is definitely suitable for the semiquantification of these genes. PAMG induces the increase of the message ribonucleic acid (mRNA) expression of c-myc, while the p53 and beta-actin remain even. This change is not related to the concentration of AM in the gel and may be incited by other components in the extract of PMAG. PMID:16637045

  10. Exploratory data analysis groupware for qualitative and quantitative electrophoretic gel analysis over the Internet-WebGel.

    PubMed

    Lemkin, P F; Myrick, J M; Lakshmanan, Y; Shue, M J; Patrick, J L; Hornbeck, P V; Thornwal, G C; Partin, A W

    1999-12-01

    Many scientists use quantitative measurements to compare the presence and amount, of various proteins and nucleotides among series of one- and two-dimensional (1-D and 2-D) electrophoretic gels. These gels are often scanned into digital image files. Gel spots are then quantified using stand-alone analysis software. However, as more research collaborations take place over the Internet, it has become useful to share intermediate quantitative data between researchers. This allows research group members to investigate their data and share their work in progress. We developed a World Wide Web group-accessible software system, WebGel, for interactively exploring qualitative and quantitative differences between electrophoretic gels. Such Internet databases are useful for publishing quantitative data and allow other researchers to explore the data with respect to their own research. Because intermediate results of one user may be shared with their collaborators using WebGel, this form of active data-sharing constitutes a groupware method for enhancing collaborative research. Quantitative and image gel data from a stand-alone gel image processing system are copied to a database accessible on the WebGel Web server. These data are then available for analysis by the WebGel database program residing on that server. Visualization is critical for better understanding of the data. WebGel helps organize labeled gel images into montages of corresponding spots as seen in these different gels. Various views of multiple gel images, including sets of spots, normalization spots, labeled spots, segmented gels, etc. may also be displayed. These displays are active and may be used for performing database operations directly on individual protein spots by simply clicking on them. Corresponding regions between sets of gels may be visually analyzed using Flicker-comparison (Electrophoresis 1997, 18, 122-140) as one of the WebGel methods for qualitative analysis. Quantitative exploratory data

  11. A new inversion method for (T2, D) 2D NMR logging and fluid typing

    NASA Astrophysics Data System (ADS)

    Tan, Maojin; Zou, Youlong; Zhou, Cancan

    2013-02-01

    One-dimensional nuclear magnetic resonance (1D NMR) logging technology has some significant limitations in fluid typing. However, not only can two-dimensional nuclear magnetic resonance (2D NMR) provide some accurate porosity parameters, but it can also identify fluids more accurately than 1D NMR. In this paper, based on the relaxation mechanism of (T2, D) 2D NMR in a gradient magnetic field, a hybrid inversion method that combines least-squares-based QR decomposition (LSQR) and truncated singular value decomposition (TSVD) is examined in the 2D NMR inversion of various fluid models. The forward modeling and inversion tests are performed in detail with different acquisition parameters, such as magnetic field gradients (G) and echo spacing (TE) groups. The simulated results are discussed and described in detail, the influence of the above-mentioned observation parameters on the inversion accuracy is investigated and analyzed, and the observation parameters in multi-TE activation are optimized. Furthermore, the hybrid inversion can be applied to quantitatively determine the fluid saturation. To study the effects of noise level on the hybrid method and inversion results, the numerical simulation experiments are performed using different signal-to-noise-ratios (SNRs), and the effect of different SNRs on fluid typing using three fluid models are discussed and analyzed in detail.

  12. Two-dimensional fluorescence difference gel electrophoresis for comparative proteomics profiling

    PubMed Central

    Tannu, Nilesh S; Hemby, Scott E

    2007-01-01

    Quantitative proteomics is the workhorse of the modern proteomics initiative. The gel-based and MuDPIT approaches have facilitated vital advances in the measurement of protein expression alterations in normal and disease phenotypic states. The methodological advance in two-dimensional gel electrophoresis (2DGE) has been the multiplexing fluorescent two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). 2D-DIGE is based on direct labeling of lysine groups on proteins with cyanine CyDye DIGE Fluor minimal dyes before isoelectric focusing, enabling the labeling of 2–3 samples with different dyes and electrophoresis of all the samples on the same 2D gel. This capability minimizes spot pattern variability and the number of gels in an experiment while providing simple, accurate and reproducible spot matching. This protocol can be completed in 3–5 weeks depending on the sample size of the experiment and the level of expertise of the investigator. PMID:17487156

  13. Radiofrequency Spectroscopy and Thermodynamics of Fermi Gases in the 2D to Quasi-2D Dimensional Crossover

    NASA Astrophysics Data System (ADS)

    Cheng, Chingyun; Kangara, Jayampathi; Arakelyan, Ilya; Thomas, John

    2016-05-01

    We tune the dimensionality of a strongly interacting degenerate 6 Li Fermi gas from 2D to quasi-2D, by adjusting the radial confinement of pancake-shaped clouds to control the radial chemical potential. In the 2D regime with weak radial confinement, the measured pair binding energies are in agreement with 2D-BCS mean field theory, which predicts dimer pairing energies in the many-body regime. In the qausi-2D regime obtained with increased radial confinement, the measured pairing energy deviates significantly from 2D-BCS theory. In contrast to the pairing energy, the measured radii of the cloud profiles are not fit by 2D-BCS theory in either the 2D or quasi-2D regimes, but are fit in both regimes by a beyond mean field polaron-model of the free energy. Supported by DOE, ARO, NSF, and AFOSR.

  14. Northwestern Blot Analysis: Detecting RNA-Protein Interaction After Gel Separation of Protein Mixture.

    PubMed

    Zang, Shangbing; Lin, Ren-Jang

    2016-01-01

    Northwestern assays detect a direct binding of a given RNA molecule to a protein immobilized on a nitrocellulose membrane. Here, we describe protocols to prepare (32)P-labeled RNA probes and to use them to assay for RNA-protein interactions after partially purified protein preparations are resolved on denaturing SDS-polyacrylamide gels. The method can unambiguously determine whether the protein of interest can directly and independently bind RNA even in the presence of contaminating bacterial proteins or degradation products that at times may hinder interpretation of results obtained from gel mobility shift or RNP immunoprecipitation assays. PMID:26965261

  15. Competing coexisting phases in 2D water

    PubMed Central

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-01-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules. PMID:27185018

  16. 2D Radiative Processes Near Cloud Edges

    NASA Technical Reports Server (NTRS)

    Varnai, T.

    2012-01-01

    Because of the importance and complexity of dynamical, microphysical, and radiative processes taking place near cloud edges, the transition zone between clouds and cloud free air has been the subject of intense research both in the ASR program and in the wider community. One challenge in this research is that the one-dimensional (1D) radiative models widely used in both remote sensing and dynamical simulations become less accurate near cloud edges: The large horizontal gradients in particle concentrations imply that accurate radiative calculations need to consider multi-dimensional radiative interactions among areas that have widely different optical properties. This study examines the way the importance of multidimensional shortwave radiative interactions changes as we approach cloud edges. For this, the study relies on radiative simulations performed for a multiyear dataset of clouds observed over the NSA, SGP, and TWP sites. This dataset is based on Microbase cloud profiles as well as wind measurements and ARM cloud classification products. The study analyzes the way the difference between 1D and 2D simulation results increases near cloud edges. It considers both monochromatic radiances and broadband radiative heating, and it also examines the influence of factors such as cloud type and height, and solar elevation. The results provide insights into the workings of radiative processes and may help better interpret radiance measurements and better estimate the radiative impacts of this critical region.

  17. Simulation of Yeast Cooperation in 2D.

    PubMed

    Wang, M; Huang, Y; Wu, Z

    2016-03-01

    Evolution of cooperation has been an active research area in evolutionary biology in decades. An important type of cooperation is developed from group selection, when individuals form spatial groups to prevent them from foreign invasions. In this paper, we study the evolution of cooperation in a mixed population of cooperating and cheating yeast strains in 2D with the interactions among the yeast cells restricted to their small neighborhoods. We conduct a computer simulation based on a game theoretic model and show that cooperation is increased when the interactions are spatially restricted, whether the game is of a prisoner's dilemma, snow drifting, or mutual benefit type. We study the evolution of homogeneous groups of cooperators or cheaters and describe the conditions for them to sustain or expand in an opponent population. We show that under certain spatial restrictions, cooperator groups are able to sustain and expand as group sizes become large, while cheater groups fail to expand and keep them from collapse. PMID:26988702

  18. Phase Engineering of 2D Tin Sulfides.

    PubMed

    Mutlu, Zafer; Wu, Ryan J; Wickramaratne, Darshana; Shahrezaei, Sina; Liu, Chueh; Temiz, Selcuk; Patalano, Andrew; Ozkan, Mihrimah; Lake, Roger K; Mkhoyan, K A; Ozkan, Cengiz S

    2016-06-01

    Tin sulfides can exist in a variety of phases and polytypes due to the different oxidation states of Sn. A subset of these phases and polytypes take the form of layered 2D structures that give rise to a wide host of electronic and optical properties. Hence, achieving control over the phase, polytype, and thickness of tin sulfides is necessary to utilize this wide range of properties exhibited by the compound. This study reports on phase-selective growth of both hexagonal tin (IV) sulfide SnS2 and orthorhombic tin (II) sulfide SnS crystals with diameters of over tens of microns on SiO2 substrates through atmospheric pressure vapor-phase method in a conventional horizontal quartz tube furnace with SnO2 and S powders as the source materials. Detailed characterization of each phase of tin sulfide crystals is performed using various microscopy and spectroscopy methods, and the results are corroborated by ab initio density functional theory calculations. PMID:27099950

  19. Ion Transport in 2-D Graphene Nanochannels

    NASA Astrophysics Data System (ADS)

    Xie, Quan; Foo, Elbert; Duan, Chuanhua

    2015-11-01

    Graphene membranes have recently attracted wide attention due to its great potential in water desalination and selective molecular sieving. Further developments of these membranes, including enhancing their mass transport rate and/or molecular selectivity, rely on the understanding of fundamental transport mechanisms through graphene membranes, which has not been studied experimentally before due to fabrication and measurement difficulties. Herein we report the fabrication of the basic constituent of graphene membranes, i.e. 2-D single graphene nanochannels (GNCs) and the study of ion transport in these channels. A modified bonding technique was developed to form GNCs with well-defined geometry and uniform channel height. Ion transport in such GNCs was studied using DC conductance measurement. Our preliminary results showed that the ion transport in GNCs is still governed by surface charge at low concentrations (10-6M to 10-4M). However, GNCs exhibits much higher ionic conductances than silica nanochannels with the same geometries in the surface-charge-governed regime. This conductance enhancement can be attributed to the pre-accumulation of charges on graphene surfaces. The work is supported by the Faculty Startup Fund (Boston University, USA).

  20. Parallel map analysis on 2-D grids

    SciTech Connect

    Berry, M.; Comiskey, J.; Minser, K.

    1993-12-31

    In landscape ecology, computer modeling is used to assess habitat fragmentation and its ecological iMPLications. Specifically, maps (2-D grids) of habitat clusters must be analyzed to determine number, sizes and geometry of clusters. Models prior to this study relied upon sequential Fortran-77 programs which limited the sizes of maps and densities of clusters which could be analyzed. In this paper, we present more efficient computer models which can exploit recursion or parallelism. Significant improvements over the original Fortran-77 programs have been achieved using both recursive and nonrecursive C implementations on a variety of workstations such as the Sun Sparc 2, IBM RS/6000-350, and HP 9000-750. Parallel implementations on a 4096-processor MasPar MP-1 and a 32-processor CM-5 are also studied. Preliminary experiments suggest that speed improvements for the parallel model on the MasPar MP-1 (written in MPL) and on the CM-5 (written in C using CMMD) can be as much as 39 and 34 times faster, respectively, than the most efficient sequential C program on a Sun Sparc 2 for a 512 map. An important goal in this research effort is to produce a scalable map analysis algorithm for the identification and characterization of clusters for relatively large maps on massively-parallel computers.

  1. 2D Turbulence with Complicated Boundaries

    NASA Astrophysics Data System (ADS)

    Roullet, G.; McWilliams, J. C.

    2014-12-01

    We examine the consequences of lateral viscous boundary layers on the 2D turbulence that arises in domains with complicated boundaries (headlands, bays etc). The study is carried out numerically with LES. The numerics are carefully designed to ensure all global conservation laws, proper boundary conditions and a minimal range of dissipation scales. The turbulence dramatically differs from the classical bi-periodic case. Boundary layer separations lead to creation of many small vortices and act as a continuing energy source exciting the inverse cascade of energy throughout the domain. The detachments are very intermittent in time. In free decay, the final state depends on the effective numerical resolution: laminar with a single dominant vortex for low Re and turbulent with many vortices for large enough Re. After very long time, the turbulent end-state exhibits a striking tendency for the emergence of shielded vortices which then interact almost elastically. In the forced case, the boundary layers allow the turbulence to reach a statistical steady state without any artificial hypo-viscosity or other large-scale dissipation. Implications are discussed for the oceanic mesoscale and submesoscale turbulence.

  2. Competing coexisting phases in 2D water

    NASA Astrophysics Data System (ADS)

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-05-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules.

  3. Competing coexisting phases in 2D water.

    PubMed

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-01-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules. PMID:27185018

  4. 2-D wavelet with position controlled resolution

    NASA Astrophysics Data System (ADS)

    Walczak, Andrzej; Puzio, Leszek

    2005-09-01

    Wavelet transformation localizes all irregularities in the scene. It is most effective in the case when intensities in the scene have no sharp details. It is the case often present in a medical imaging. To identify the shape one has to extract it from the scene as typical irregularity. When the scene does not contain sharp changes then common differential filters are not efficient tool for a shape extraction. The new 2-D wavelet for such task has been proposed. Described wavelet transform is axially symmetric and has varied scale in dependence on the distance from the centre of the wavelet symmetry. The analytical form of the wavelet has been presented as well as its application for details extraction in the scene. Most important feature of the wavelet transform is that it gives a multi-scale transformation, and if zoom is on the wavelet selectivity varies proportionally to the zoom step. As a result, the extracted shape does not change during zoom operation. What is more the wavelet selectivity can be fit to the local intensity gradient properly to obtain best extraction of the irregularities.

  5. Facial Gel Complication after Dental Injection: A Case Report

    PubMed Central

    Pourdanesh, Fereydoun; Shams, Shahin; Sadeghi, Hasan Mir Mohammad

    2013-01-01

    Injectable gel is becoming increasingly popular for cosmetic reasons. The polyacrylamide gel (PAAG) is a permanent filler material used worldwide. In spite of the fact that the filler materials used today are considered quite safe, various complications have been reported in the literature. Hence PAAG use in the United States is not popular. As the area is very close to the dental field, a large complication potential is relatively considered following buccal dental injections. The aim of this article is to highlight a rare complication observed following a local anesthetic administration of a simple molar restoration in a healthy 33-year-old woman who had history of a filler augmentation in her cheek approximately 6 years ago. PMID:24436772

  6. Facial gel complication after dental injection: a case report.

    PubMed

    Pourdanesh, Fereydoun; Shams, Shahin; Sadeghi, Hasan Mir Mohammad

    2013-12-01

    Injectable gel is becoming increasingly popular for cosmetic reasons. The polyacrylamide gel (PAAG) is a permanent filler material used worldwide. In spite of the fact that the filler materials used today are considered quite safe, various complications have been reported in the literature. Hence PAAG use in the United States is not popular. As the area is very close to the dental field, a large complication potential is relatively considered following buccal dental injections. The aim of this article is to highlight a rare complication observed following a local anesthetic administration of a simple molar restoration in a healthy 33-year-old woman who had history of a filler augmentation in her cheek approximately 6 years ago. PMID:24436772

  7. 2-D Animation's Not Just for Mickey Mouse.

    ERIC Educational Resources Information Center

    Weinman, Lynda

    1995-01-01

    Discusses characteristics of two-dimensional (2-D) animation; highlights include character animation, painting issues, and motion graphics. Sidebars present Silicon Graphics animations tools and 2-D animation programs for the desktop computer. (DGM)

  8. Fluid diversion and sweep improvement with chemical gels in oil recovery processes. Final report

    SciTech Connect

    Seright, R.S.; Martin, F.D.

    1992-09-01

    The objectives of this project were to identify the mechanisms by which gel treatments divert fluids in reservoirs and to establish where and how gel treatments are best applied. Several different types of gelants were examined, including polymer-based gelants, a monomer-based gelant, and a colloidal-silica gelant. This research was directed at gel applications in water injection wells, in production wells, and in high-pressure gas floods. The work examined how the flow properties of gels and gelling agents are influenced by permeability, lithology, and wettability. Other goals included determining the proper placement of gelants, the stability of in-place gels, and the types of gels required for the various oil recovery processes and for different scales of reservoir heterogeneity. During this three-year project, a number of theoretical analyses were performed to determine where gel treatments are expected to work best and where they are not expected to be effective. The most important, predictions from these analyses are presented. Undoubtedly, some of these predictions will be controversial. However, they do provide a starting point in establishing guidelines for the selection of field candidates for gel treatments. A logical next step is to seek field data that either confirm or contradict these predictions. The experimental work focused on four types of gels: (1) resorcinol-formaldehyde, (2) colloidal silica, (3) Cr{sup 3+}(chloride)-xanthan, and (4) Cr{sup 3+}(acetate)-polyacrylamide. All experiments were performed at 41{degrees}C.

  9. MAZE96. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Sanford, L.; Hallquist, J.O.

    1992-02-24

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  10. On 2D graphical representation of DNA sequence of nondegeneracy

    NASA Astrophysics Data System (ADS)

    Zhang, Yusen; Liao, Bo; Ding, Kequan

    2005-08-01

    Some two-dimensional (2D) graphical representations of DNA sequences have been given by Gates, Nandy, Leong and Mogenthaler, Randić, and Liao et al., which give visual characterizations of DNA sequences. In this Letter, we introduce a nondegeneracy 2D graphical representation of DNA sequence, which is different from Randić's novel 2D representation and Liao's 2D representation. We also present the nondegeneracy forms corresponding to the representations of Gates, Nandy, Leong and Mogenthaler.

  11. Generates 2D Input for DYNA NIKE & TOPAZ

    1996-07-15

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  12. Neurite outgrowth at the interface of 2D and 3D growth environments

    NASA Astrophysics Data System (ADS)

    Kofron, Celinda M.; Fong, Vivian J.; Hoffman-Kim, Diane

    2009-02-01

    Growing neurons navigate complex environments, but in vitro systems for studying neuronal growth typically limit the cues to flat surfaces or a single type of cue, thereby limiting the resulting growth. Here we examined the growth of neurons presented with two-dimensional (2D) substrate-bound cues when these cues were presented in conjunction with a more complex three-dimensional (3D) architecture. Dorsal root ganglia (DRG) explants were cultured at the interface between a collagen I matrix and a glass coverslip. Laminin (LN) or chondroitin sulfate proteoglycans (CSPG) were uniformly coated on the surface of the glass coverslip or patterned in 50 µm tracks by microcontact printing. Quantitative analysis of neurite outgrowth with a novel grid system at multiple depths in the gel revealed several interesting trends. Most of the neurites extended at the surface of the gel when LN was presented whereas more neurites extended into the gel when CSPG was presented. Patterning of cues did not affect neurite density or depth of growth. However, neurite outgrowth near the surface of the gel aligned with LN patterns, and these extensions were significantly longer than neurites extended in other cultures. In interface cultures, DRG growth patterns varied with the type of cue where neurite density was higher in cultures presenting LN than in cultures presenting CSPG. These results represent an important step toward understanding how neurons integrate local structural and chemical cues to make net growth decisions.

  13. 2d PDE Linear Symmetric Matrix Solver

    1983-10-01

    ICCG2 (Incomplete Cholesky factorized Conjugate Gradient algorithm for 2d symmetric problems) was developed to solve a linear symmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as resistive MHD, spatial diffusive transport, and phase space transport (Fokker-Planck equation) problems. These problems share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized withmore » finite-difference or finite-element methods,the resulting matrix system is frequently of block-tridiagonal form. To use ICCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. The incomplete Cholesky conjugate gradient algorithm is used to solve the linear symmetric matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For matrices lacking symmetry, ILUCG2 should be used. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  14. 2d PDE Linear Asymmetric Matrix Solver

    1983-10-01

    ILUCG2 (Incomplete LU factorized Conjugate Gradient algorithm for 2d problems) was developed to solve a linear asymmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as plasma diffusion, equilibria, and phase space transport (Fokker-Planck equation) problems. These equations share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized with finite-difference or finite-elementmore » methods, the resulting matrix system is frequently of block-tridiagonal form. To use ILUCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. A generalization of the incomplete Cholesky conjugate gradient algorithm is used to solve the matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For problems having a symmetric matrix ICCG2 should be used since it runs up to four times faster and uses approximately 30% less storage. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source, containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  15. Ultrasonic 2D matrix PVDF transducer

    NASA Astrophysics Data System (ADS)

    Ptchelintsev, A.; Maev, R. Gr.

    2000-05-01

    During the past decade a substantial amount of work has been done in the area of ultrasonic imaging technology using 2D arrays. The main problems arising for the two-dimensional matrix transducers at megahertz frequencies are small size and huge count of the elements, high electrical impedance, low sensitivity, bad SNR and slower data acquisition rate. The major technological difficulty remains the high density of the interconnect. To solve these problems numerous approaches have been suggested. In the present work, a 24×24 elements (24 transmit+24 receive) matrix and a switching board were developed. The transducer consists of two 52 μm PVDF layers each representing a linear array of 24 elements placed one on the top of the other. Electrodes in these two layers are perpendicular and form the grid of 0.5×0.5 mm pitch. The layers are bonded together with the ground electrode being monolithic and located between the layers. The matrix is backed from the rear surface with an epoxy composition. During the emission, a linear element from the emitting layer generates a longitudinal wave pulse propagating inside the test object. Reflected pulses are picked-up by the receiving layer. During one transmit-receive cycle one transmit element and one receive element are selected by corresponding multiplexers. These crossed elements emulate a small element formed by their intersection. The present design presents the following advantages: minimizes number of active channels and density of the interconnect; reduces the electrical impedance of the element improving electrical matching; enables the transmit-receive mode; due to the efficient backing provides bandwidth and good time resolution; and, significantly reduces the electronics complexity. The matrix can not be used for the beam steering and focusing. Owing to this impossibility of focusing, the penetration depth is limited as well by the diffraction phenomena.

  16. 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.

  17. A Planar Quantum Transistor Based on 2D-2D Tunneling in Double Quantum Well Heterostructures

    SciTech Connect

    Baca, W.E.; Blount, M.A.; Hafich, M.J.; Lyo, S.K.; Moon, J.S.; Reno, J.L.; Simmons, J.A.; Wendt, J.R.

    1998-12-14

    We report on our work on the double electron layer tunneling transistor (DELTT), based on the gate-control of two-dimensional -- two-dimensional (2D-2D) tunneling in a double quantum well heterostructure. While previous quantum transistors have typically required tiny laterally-defined features, by contrast the DELTT is entirely planar and can be reliably fabricated in large numbers. We use a novel epoxy-bond-and-stop-etch (EBASE) flip-chip process, whereby submicron gating on opposite sides of semiconductor epitaxial layers as thin as 0.24 microns can be achieved. Because both electron layers in the DELTT are 2D, the resonant tunneling features are unusually sharp, and can be easily modulated with one or more surface gates. We demonstrate DELTTs with peak-to-valley ratios in the source-drain I-V curve of order 20:1 below 1 K. Both the height and position of the resonant current peak can be controlled by gate voltage over a wide range. DELTTs with larger subband energy offsets ({approximately} 21 meV) exhibit characteristics that are nearly as good at 77 K, in good agreement with our theoretical calculations. Using these devices, we also demonstrate bistable memories operating at 77 K. Finally, we briefly discuss the prospects for room temperature operation, increases in gain, and high-speed.

  18. Polyacrylamide hydrogel injection for breast augmentation: Another injectable failure

    PubMed Central

    Wang, Zhenxiang; Li, Shirong; Wang, Lingli; Zhang, Shu; Jiang, Yan; Chen, Jinping; Luo, Donglin

    2012-01-01

    Summary Background Increasing complications of polyacrylamide hydrogel (PAAG) augmentation mammoplasty, such as chronic persistent infection, have recently caught the attention of both the medical field and the general public. Material/Methods A total of 96 patients with severe chronic infection following PAAG augmentation mammoplasty were treated in the present study including 63 cases with infection confined to the breast and 33 with systemic infection. Endoscopy and surgery were performed to completely remove the materials and clear the infected tissues followed by drug-irrigation and vacuum-assisted closure for several days. Results In patients with severe infection there were large amounts of PAAG, fibers and infiltration of numerous neutrophils and macrophages. The infection-inducing materials were extensively dispersed in the mammary and subcutaneous tissues, pectoral fascia and intermuscular space. In addition, there was scattered distribution of PAAG materials in the armpit, chest wall and abdominal wall, which were mixed with necrotic tissues and surrounded by lymphocytes, giant cells, macrophages and other inflammatory cells, forming chronic granulomatous and fibrous lesions. Infection was controlled following surgical intervention. No residual infectious foci or recurrent infections were noted among these patients. Although the severe infection did not result in mastectomy, patients had breast atrophy and various degrees of deformation. Conclusions Chronic infection following PAAG augmentation mammaplasty usually causes systemic infection and other devastating adverse reactions. This study confirms PAAG augmentation mammaplasty is another failed attempt. More attention should be paid to the injection of large doses of liquid filler. PMID:22648256

  19. Polyacrylamide medium for the electrophoretic separation of biomolecules

    DOEpatents

    Madabhushi, Ramakrishna S.; Gammon, Stuart A.

    2003-11-11

    A polyacryalmide medium for the electrophoretic separation of biomolecules. The polyacryalmide medium comprises high molecular weight polyacrylamides (PAAm) having a viscosity average molecular weight (M.sub.v) of about 675-725 kDa were synthesized by conventional red-ox polymerization technique. Using this separation medium, capillary electrophoresis of BigDye DNA sequencing standard was performed. A single base resolution of .about.725 bases was achieved in .about.60 minute in a non-covalently coated capillary of 50 .mu.m i.d., 40 cm effective length, and a filed of 160 V/cm at 40.degree. C. The resolution achieved with this formulation to separate DNA under identical conditions is much superior (725 bases vs. 625 bases) and faster (60 min. vs. 75 min.) to the commercially available PAAm, such as supplied by Amersham. The formulation method employed here to synthesize PAAm is straight-forward, simple and does not require cumbersome methods such as emulsion polymerizaiton in order to achieve very high molecular weights. Also, the formulation here does not require separation of PAAm from the reaction mixture prior to reconstituting the polymer to a final concentration. Furthermore, the formulation here is prepared from a single average mol. wt. PAAm as opposed to the mixture of two different average mo. wt. PAAm previously required to achieve high resolution.

  20. Stereoregular polyacrylamide and its copolymer brushes: Preparation and surface characters

    NASA Astrophysics Data System (ADS)

    Jiang, Jianguo; Wang, Xiaoshu; Lu, Xiaoyan; Lu, Yun

    2008-12-01

    Two kinds of polymer brushes, the single one with stereospecific polyacrylamide (PAAM) chains and the dual-component one with random poly(methyl methacrylate) (PMMA) segments grafting from stereospecific PAAM chains, were prepared on silicon wafer for the first time by combining the immobilization of initiator and the stereospecific living radical in situ polymerization. With the addition of the Lewis acid AlCl 3 into the polymerization system, the PAAM brushes obtained exhibited an increased stereospecificity as well as a decreased hydrophilicity, which might attribute to the reduced thickness of PAAM brushes on the silicon wafer and the handicap of the free rotation of the stereospecific molecular chain. The smoother surface morphology of the stereospecific PAAM brushes shown in AFM images was in good agreement with the experimental data of water contact angle. Also, block amphiphilic copolymer brushes were prepared with the stereospecific PAAM formed first on silicon wafer as the anchored-initiator and revealed a novel surface self-assembly behavior after being treated with different solvent such as toluene or water. The stereospecificity of PAAM chains in the polymer brushes could be modulated by adjusting reaction conditions according to the requirement of applications for surface hydrophilicity.

  1. Correlated Electron Phenomena in 2D Materials

    NASA Astrophysics Data System (ADS)

    Lambert, Joseph G.

    In this thesis, I present experimental results on coherent electron phenomena in layered two-dimensional materials: single layer graphene and van der Waals coupled 2D TiSe2. Graphene is a two-dimensional single-atom thick sheet of carbon atoms first derived from bulk graphite by the mechanical exfoliation technique in 2004. Low-energy charge carriers in graphene behave like massless Dirac fermions, and their density can be easily tuned between electron-rich and hole-rich quasiparticles with electrostatic gating techniques. The sharp interfaces between regions of different carrier densities form barriers with selective transmission, making them behave as partially reflecting mirrors. When two of these interfaces are set at a separation distance within the phase coherence length of the carriers, they form an electronic version of a Fabry-Perot cavity. I present measurements and analysis of multiple Fabry-Perot modes in graphene with parallel electrodes spaced a few hundred nanometers apart. Transition metal dichalcogenide (TMD) TiSe2 is part of the family of materials that coined the term "materials beyond graphene". It contains van der Waals coupled trilayer stacks of Se-Ti-Se. Many TMD materials exhibit a host of interesting correlated electronic phases. In particular, TiSe2 exhibits chiral charge density waves (CDW) below TCDW ˜ 200 K. Upon doping with copper, the CDW state gets suppressed with Cu concentration, and CuxTiSe2 becomes superconducting with critical temperature of T c = 4.15 K. There is still much debate over the mechanisms governing the coexistence of the two correlated electronic phases---CDW and superconductivity. I will present some of the first conductance spectroscopy measurements of proximity coupled superconductor-CDW systems. Measurements reveal a proximity-induced critical current at the Nb-TiSe2 interfaces, suggesting pair correlations in the pure TiSe2. The results indicate that superconducting order is present concurrently with CDW in

  2. Investigation of the properties of polyacrylamide-polyaniline composite and its application as a battery electrode

    SciTech Connect

    Bhat, N.V.; Joshi, N.V. . Dept. of Chemical Technology)

    1993-11-20

    The composite films of polyacrylamide and polyaniline were prepared by polymerizing aniline using ammonium persulfate as an initiator in an aqueous solution containing poly-acrylamide. A film was then cast from this solution. The structural, dynamic mechanical, electrical, and thermal properties of these films have been studied. The infrared spectrum shows the presence of polyacrylamide as well as polyaniline in the composite film. The thermal analysis shows that the composite degrades slower than does the polyacrylamide alone. The dynamic mechanical analysis indicates that there is an increase in the glass transition temperature after the composite formation. The electrical conductivity has been found to increase by more than eight orders of magnitude. These composite films have also been suitably used as electrodes in secondary batteries.

  3. 21 CFR 872.3420 - Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... comfort. (b) Classification. Class III. (c) Date PMA or notice of completion of a PDP is required. A PMA... carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive shall have an approved PMA or...

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

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... comfort. (b) Classification. Class III. (c) Date PMA or notice of completion of a PDP is required. A PMA... carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive shall have an approved PMA or...

  5. Development of Polymer Gel Systems to Improve Volumetric Sweep and Reduce Producing Water/Oil Ratios

    SciTech Connect

    G. Paul Willhite; Stan McCool; Don W. Green; Min Cheng; Feiyan Chen

    2005-04-03

    Gelled polymer treatments are applied to oil reservoirs to increase oil production and to reduce water production by altering the fluid movement within the reservoir. This report describes the results of the third year of a 42 month research program that is aimed at an understanding of gelation chemistry and the fundamental mechanisms that alter the flows of oil and water in reservoir rocks after a gel treatment. Work focused on a widely applied system in the field, the partially hydrolyzed polyacrylamide-chromium acetate gel. Gelation occurs by network formation through the crosslinking of polyacrylamide molecules as a result of reaction with chromium acetate. Pre-gel aggregates form and grow as reactions between chromium acetate and polyacrylamide proceed. A mathematical model that describes uptake and crosslinking reactions as a function of time was derived. The model was probability based and provides molecular-weight averages and molecular-weight distributions of the pre-gel aggregates as a function of time and initial system conditions. A liquid chromatography apparatus to experimentally measure the size and molecular weight distributions of polymer samples was developed. The method worked well for polymer samples without the chromium crosslinker. Sample retention observed during measurements of gelant samples during the gelation process compromised the results. Other methods will be tested to measure size distributions of the pre-gel aggregates. Dissolution of carbonate minerals during the injection of gelants causes the pH of the gelant to increase. Chromium precipitates from solution at the higher pH values robbing the gelant of crosslinker. Experimental data on the transport of chromium acetate solutions through dolomite cores were obtained. A mathematical model that describes the transport of brine and chromium acetate solutions through rocks containing carbonate minerals was used to simulate the experimental results.

  6. Characterization of the c-type cytochromes of Nitrosomonas europaea with the aid of fluorescent gels

    PubMed Central

    Miller, David J.; Wood, Paul M.

    1982-01-01

    When a total soluble extract of Nitrosomonas europaea was denatured with dodecyl sulphate, subjected to dodecyl sulphate/polyacrylamide-gel electrophoresis and illuminated with near-u.v. light, eight bands of protein fluorescence were observed. All but one of these bands were red in colour, a property characteristic of c-type cytochromes. Standard techniques were used to purify soluble c-type cytochromes from this organism, and it was then possible to assign all but two very minor bands to specific c-type cytochromes, namely hydroxylamine oxidase, cytochrome c-554, cytochrome c-552 and a cytochrome c-550 not previously described. The eight band had fluorescence peaking in the green region of the spectrum, probably caused by covalently bound flavin, and co-purified with hydroxylamine oxidase. The following physical properties were determined for these components: isoelectric point, molecular weights according to gel filtration and mobility on dodecyl sulphate/polyacrylamide gels, and α-band spectra at room temperature and 77K. Redox potentials were measured as follows: cytochrome c-554, Em,7 = +20mV; cytochrome c-552, Em,7 = +230mV; cytochrome c-550, Em,7 = +140mV. When washed membranes were applied to dodecyl sulphate/polyacrylamide gels in the same way, a number of fluorescent bands were observed that could be matched by soluble proteins. In addition, there was one band that could not be detected in supernatants, migrating with an apparent molecular weight of 24000. This species is probably coincident with a c-type cytochrome having Em,7 = +170mV found in redox titration of these membranes. In future studies, gel fluorescence should form a useful complement to spectroscopy for analysis of cytochrome composition in active cell-free preparations or semi-purified material. PMID:6299271

  7. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6*15 and *35 Genotyping

    PubMed Central

    Riffel, Amanda K.; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C.; Leeder, J. Steven; Rosenblatt, Kevin P.; Gaedigk, Andrea

    2016-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact

  8. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping.

    PubMed

    Riffel, Amanda K; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C; Leeder, J Steven; Rosenblatt, Kevin P; Gaedigk, Andrea

    2015-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6 (*) 15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6 (*) 15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6 (*) 35) which is also located in exon 1. Although alternative CYP2D6 (*) 15 and (*) 35 assays resolved the issue, we discovered a novel CYP2D6 (*) 15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6 (*) 15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6 (*) 43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer

  9. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    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 analysis 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 of

  10. 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

  11. 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

    2015-01-01

    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

  12. Polyacrylamide added as a nitrogen source stimulates methanogenesis in consortia from various wastewaters.

    PubMed

    Haveroen, Melissa E; MacKinnon, Michael D; Fedorak, Phillip M

    2005-09-01

    Polyacrylamides are widely used as flocculants to enhance clarification of drinking waters and domestic wastewaters, for stabilization of agricultural soils, and to aid in managing mine tailings. The flocs produced with polyacrylamide may be deposited into retention areas that become anaerobic. Although it is unlikely that the carbon backbone of these polymers would be cleaved by microbial activity, the amide group could serve as a nitrogen source for microorganisms. Previous studies have shown that aerobic bacteria utilize the nitrogen from polyacrylamide. This study assessed whether methanogenesis was stimulated when an anionic polyacrylamide (Magnafloc LT27AG) was the sole fixed nitrogen source in serum-bottle microcosms. Microorganisms from two oil sands tailings sources, and a domestic anaerobic sewage sludge were used, with benzoate or acetate provided as carbon and energy sources. In each inoculum-substrate combination, the presence of polyacrylamide-enhanced methane production, indicating that polyacrylamide may stimulate microbial activities in anaerobic environments that are rich in fermentable carbon, but lack nitrogen sources. PMID:16023701

  13. High-Frequency Alternating-Crossed-Field Gel Electrophoresis WithNeutral or Slightly Charged Interpenetrating Networks to Improve DNASeparation

    SciTech Connect

    Boyd, B.; Prausnitz, J.; Blanch, H.

    1998-07-01

    Toward improving DNA separations, this work reports theeffects of high-frequency square-wave AC fields superimposedperpendicular to the direct current (DC) separation field on DNAmigration in both polyacrylamide-based interpenetrating networks (IPNs)and in agarose networks. Compared to standard polyacrylamide gels, IPNsallow the separation of larger DNA (9000 bp vs. 5000 bp at 5 V/cm). Innovel polyacrylamide-based IPNs, an alternating current (AC) field of 5Hz increased the maximum DNA size separable. This effect was extended tolarger DNA sizes with increasing electric-field strength up to andapparently beyond the power supply-limited maximum electric-fieldstrength of 48 V/cm. The orthogonal AC field also increased mobility.These two results combine to yield a reduction in separation time of upto a factor of 20 in novel polyacrylamide-based IPNs. When negativelycharged acrylic-acid groups were incorporated into the IPNs, the use ofthe AC field changed the DNA-network interaction, which altered the sizedependence of DNA mobility. In agarose gels, an AC field of 50 Hzincreased the size range separable; however, there was no increase in DNAmobility. There was no change in size dependence of mobility in an ACfield when the number of charged groups in the agarose network wasincreased. Based on results in the literature, possible mechanisms wereexamined for the effects of the AC field on DNA separation.

  14. 2D-PAGE protein analysis of dinoflagellate Alexandrium minutum based on three different temperatures

    NASA Astrophysics Data System (ADS)

    Latib, Norhidayu Abdul; Norshaha, Safida Anira; Usup, Gires; Yusof, Nurul Yuziana Mohd

    2015-09-01

    Harmful algae bloom or red tide seems to be considered as threat to ecosystem, especially to human consumption because of the production of neurotoxin by dinoflagellates species such as Alexandrium minutum which can lead to paralytic shellfish poisoning. The aim of this study is to determine the most suitable method for protein extraction of A. minutum followed by determination of differential protein expression of A. minutum on three different temperatures (15°C, 26°C and 31.5°C). After the optimization, the protein extract was subjected to two-dimensional polyacrylamide gel electrophoresis (2-DE) to compare the intensity and distribution of the protein spots. Based on quantitative and qualitative protein assessment, use of Trizol reagent is the most suitable method to extract protein from A. minutum. 2-DE analysis of the samples results in different distribution and intensity of the protein spots were compared between 15°C, 26°C and 31.5°C.

  15. Application of a PAGAT/MgCl2 gel for dose measurements in a 150 MeV proton beam

    NASA Astrophysics Data System (ADS)

    Tominaga, T.; Hayashi, S.; Usui, S.; Kawamura, H.; Katahira, K.

    2013-06-01

    The purpose of this study is to evaluate the dose response of polyacrylamide-based gel (PAGAT) when irradiated with clinical proton beams. Recently inorganic salt additive in gel has been reported to improve dose sensitivity substantially. We attempted to add MgCl2 (0.5M) to regular PAGAT gel in order to compensate its lower radiation sensitivity. The spin-spin relaxation rates (R2) as dose readout was calculated from MR imaging after irradiation with 150MeV proton beam. The dose sensitivity was discussed from the slope at dose-R2 response curve. As the result, the sensitivity of the gel with MgCl2 is approximately 3 times higher than that of regular PAGAT gel without spoiling dose response stability under the various irradiation conditions such as dose rate and dose integration.

  16. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2004-09-30

    This report describes work performed during the third and final year of the project, ''Conformance Improvement Using Gels.'' Corefloods revealed throughput dependencies of permeability reduction by polymers and gels that were much more prolonged during oil flow than water flow. This behavior was explained using simple mobility ratio arguments. A model was developed that quantitatively fits the results and predicts ''clean up'' times for oil productivity when production wells are returned to service after application of a polymer or gel treatment. X-ray computed microtomography studies of gels in strongly water-wet Berea sandstone and strongly oil-wet porous polyethylene suggested that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than gel-ripping or gel-displacement mechanisms. In contrast, analysis of data from the University of Kansas suggests that the gel-ripping or displacement mechanisms are more important in more permeable, strongly water-wet sandpacks. These findings help to explain why aqueous gels can reduce permeability to water more than to oil under different conditions. Since cement is the most commonly used material for water shutoff, we considered when gels are preferred over cements. Our analysis and experimental results indicated that cement cannot be expected to completely fill (top to bottom) a vertical fracture of any width, except near the wellbore. For vertical fractures with apertures less than 4 mm, the cement slurry will simply not penetrate very far into the fracture. For vertical fractures with apertures greater than 4 mm, the slurry may penetrate a substantial distance into the bottom part of the fracture. However, except near the wellbore, the upper part of the fracture will remain open due to gravity segregation. We compared various approaches to plugging fractures using gels, including (1) varying polymer content, (2) varying placement (extrusion) rate, (3) using partially formed gels, (4

  17. Probing structure-antifouling activity relationships of polyacrylamides and polyacrylates.

    PubMed

    Zhao, Chao; Zhao, Jun; Li, Xiaosi; Wu, Jiang; Chen, Shenfu; Chen, Qiang; Wang, Qiuming; Gong, Xiong; Li, Lingyan; Zheng, Jie

    2013-07-01

    We have synthesized two different polyacrylamide polymers with amide groups (polySBAA and polyHEAA) and two corresponding polyacrylate polymers without amide groups (polySBMA and polyHEA), with particular attention to the evaluation of the effect of amide group on the hydration and antifouling ability of these systems using both computational and experimental approaches. The influence of polymer architectures of brushes, hydrogels, and nanogels, prepared by different polymerization methods, on antifouling performance is also studied. SPR and ELISA data reveal that all polymers exhibit excellent antifouling ability to repel proteins from undiluted human blood serum/plasma, and such antifouling ability can be further enhanced by presenting amide groups in polySBAA and polyHEAA as compared to polySBMA and polyHEA. The antifouling performance is positively correlated with the hydration properties. Simulations confirm that four polymers indeed have different hydration characteristics, while all presenting a strong hydration overall. Integration of amide group with pendant hydroxyl or sulfobetaine group in polymer backbones is found to increase their surface hydration of polymer chains and thus to improve their antifouling ability. Importantly, we present a proof-of-concept experiment to synthesize polySBAA nanogels, which show a switchable property between antifouling and pH-responsive functions driven by acid-base conditions, while still maintaining high stability in undiluted fetal bovine serum and minimal toxicity to cultured cells. This work provides important structural insights into how very subtle structural changes in polymers can yield great improvement in biological activity, specifically the inclusion of amide group in polymer backbone/sidechain enables to obtain antifouling materials with better performance for biomedical applications. PMID:23562049

  18. Evaluating the efficacy of subcellular fractionation of blast cells using live cell labeling and 2D DIGE.

    PubMed

    Ho, Yin Ying; Penno, Megan; Perugini, Michelle; Lewis, Ian; Hoffmann, Peter

    2012-01-01

    Labeling of exposed cell surface proteins of live cells using CyDye DIGE fluor minimal dyes is an efficient strategy for cell surface proteome profiling and quantifying differentially expressed proteins in diseases. Here we describe a strategy to evaluate a two-step detergent-based protein fractionation method using live cell labeling followed by visualization of the fluorescently labeled cell surface proteins and fractionated proteins within a single 2D gel. PMID:22311770

  19. New resin gel for uranium determination by diffusive gradient in thin films technique.

    PubMed

    Gregusova, Michaela; Docekal, Bohumil

    2011-01-17

    A new resin gel based on Spheron-Oxin(®) chelating ion-exchanger with anchored 8-hydroxyquinoline functional groups was tested for application in diffusive gradient in thin film technique (DGT) for determination of uranium. Selectivity of uranium uptake from model carbonate loaded solutions of natural water was studied under laboratory conditions and compared with selectivity of the conventional Chelex 100 based resin gel. The affinity of Spheron-Oxin(®) functional groups enables determination of the overall uranium concentration in water containing carbonates up to the concentration level of 10(2) mg L(-1). The effect of uranium binding to the polyacrylamide (APA) and agarose diffusive gels (AGE) was also studied. Uranium is probably bound in both gels by a weak interaction with traces of acrylic acid groups in the structure of APA gel and with pyruvic and sulfonic acid groups in the AGE gel. These sorption effects can be eliminated to the negligible level by prolonged deployment of DGT probes or by disassembling probes after the 1-2 days post-sampling period that is sufficient for release of uranium from diffusive gel and its sorption in resin gel. PMID:21167996

  20. pI-Control in Comparative Fluorescence Gel Electrophoresis (CoFGE) using amphoteric azo dyes.

    PubMed

    Hanneken, Marina; Šlais, Karel; König, Simone

    2015-06-01

    Amphoteric azo dyes were used for internal control of pI values in Comparative two-dimensional Fluorescence Gel Electrophoresis (CoFGE) [1]. The 2D-gel images of separated Escherichia coli proteins as well as those of colored amphoteric dyes separated by isoelectric focussing are presented. The latter were used to correct for variation in the first electrophoretic dimension and further improve protein coordinate assignment in 2D-gel electrophoresis. Data tables are supplied to demonstrate pI-value calibration and the effect on the assignment of protein spot coordinates. PMID:26217748

  1. pI-Control in Comparative Fluorescence Gel Electrophoresis (CoFGE) using amphoteric azo dyes

    PubMed Central

    Hanneken, Marina; Šlais, Karel; König, Simone

    2015-01-01

    Amphoteric azo dyes were used for internal control of pI values in Comparative two-dimensional Fluorescence Gel Electrophoresis (CoFGE) [1]. The 2D-gel images of separated Escherichia coli proteins as well as those of colored amphoteric dyes separated by isoelectric focussing are presented. The latter were used to correct for variation in the first electrophoretic dimension and further improve protein coordinate assignment in 2D-gel electrophoresis. Data tables are supplied to demonstrate pI-value calibration and the effect on the assignment of protein spot coordinates. PMID:26217748

  2. Differential CYP 2D6 Metabolism Alters Primaquine Pharmacokinetics

    PubMed Central

    Potter, Brittney M. J.; Xie, Lisa H.; Vuong, Chau; Zhang, Jing; Zhang, Ping; Duan, Dehui; Luong, Thu-Lan T.; Bandara Herath, H. M. T.; Dhammika Nanayakkara, N. P.; Tekwani, Babu L.; Walker, Larry A.; Nolan, Christina K.; Sciotti, Richard J.; Zottig, Victor E.; Smith, Philip L.; Paris, Robert M.; Read, Lisa T.; Li, Qigui; Pybus, Brandon S.; Sousa, Jason C.; Reichard, Gregory A.

    2015-01-01

    Primaquine (PQ) metabolism by the cytochrome P450 (CYP) 2D family of enzymes is required for antimalarial activity in both humans (2D6) and mice (2D). Human CYP 2D6 is highly polymorphic, and decreased CYP 2D6 enzyme activity has been linked to decreased PQ antimalarial activity. Despite the importance of CYP 2D metabolism in PQ efficacy, the exact role that these enzymes play in PQ metabolism and pharmacokinetics has not been extensively studied in vivo. In this study, a series of PQ pharmacokinetic experiments were conducted in mice with differential CYP 2D metabolism characteristics, including wild-type (WT), CYP 2D knockout (KO), and humanized CYP 2D6 (KO/knock-in [KO/KI]) mice. Plasma and liver pharmacokinetic profiles from a single PQ dose (20 mg/kg of body weight) differed significantly among the strains for PQ and carboxy-PQ. Additionally, due to the suspected role of phenolic metabolites in PQ efficacy, these were probed using reference standards. Levels of phenolic metabolites were highest in mice capable of metabolizing CYP 2D6 substrates (WT and KO/KI 2D6 mice). PQ phenolic metabolites were present in different quantities in the two strains, illustrating species-specific differences in PQ metabolism between the human and mouse enzymes. Taking the data together, this report furthers understanding of PQ pharmacokinetics in the context of differential CYP 2D metabolism and has important implications for PQ administration in humans with different levels of CYP 2D6 enzyme activity. PMID:25645856

  3. Gel mobility shift assays for RNA binding viral RNAi suppressors.

    PubMed

    Csorba, Tibor; Burgyán, József

    2011-01-01

    The host-virus interaction is a continuous coevolutionary race involving both host defence strategies and virus escape mechanisms. RNA silencing is one of the main processes employed by eukaryotic organisms to fight viruses. However, viruses encode suppressor proteins to counteract this antiviral mechanism. Virtually all plant viruses encode at least one suppressor. In spite of being highly diverse at the protein level, a large group of these proteins inhibit RNA silencing very similarly, by sequestration of double-stranded RNA or small-interfering RNA molecules, the central players of the pathway. The RNA binding capacity of virus suppressor proteins can be studied by the electrophoretic mobility shift assay method. Also known as gel retardation assay, gel mobility assay, gel shift assay or band shift assay, EMSA is an in vitro technique used to characterize protein:DNA or protein:RNA interactions. The method had been developed based on the observation that protein: nucleic acid complexes migrate slower through a non-denaturing polyacrylamide gel than the free nucleic acid fragments. Here, we provide a detailed protocol for the analysis of crucifer-infecting Tobacco mosaic tobamovirus (cr-TMV) silencing suppressor protein p122 RNA binding capacity. PMID:21431690

  4. 2D to 3D to 2D Dimensionality Crossovers in Thin BSCCO Films

    NASA Astrophysics Data System (ADS)

    Williams, Gary A.

    2003-03-01

    With increasing temperature the superfluid fraction in very thin BSCCO films undergoes a series of dimensionality crossovers. At low temperatures the strong anisotropy causes the thermal excitations to be 2D pancake-antipancake pairs in uncoupled layers. At higher temperatures where the c-axis correlation length becomes larger than a layer there is a crossover to 3D vortex loops. These are initially elliptical, but as the 3D Tc is approached they become more circular as the anisotropy scales away, as modeled by Shenoy and Chattopadhyay [1]. Close to Tc when the correlation length becomes comparable to the film thickness there is a further crossover to a 2D Kosterlitz-Thouless transition, with a drop of the superfluid fraction to zero at T_KT which can be of the order of 1 K below T_c. Good agreement with this model is found for experiments on thin BSCCO 2212 films [2]. 1. S. R. Shenoy and B. Chattopadhyay, Phys. Rev. B 51, 9129 (1995). 2. K. Osborn et al., cond-mat/0204417.

  5. Mechanical characterization of 2D, 2D stitched, and 3D braided/RTM materials

    NASA Technical Reports Server (NTRS)

    Deaton, Jerry W.; Kullerd, Susan M.; Portanova, Marc A.

    1993-01-01

    Braided composite materials have potential for application in aircraft structures. Fuselage frames, floor beams, wing spars, and stiffeners are examples where braided composites could find application if cost effective processing and damage tolerance requirements are met. Another important consideration for braided composites relates to their mechanical properties and how they compare to the properties of composites produced by other textile composite processes being proposed for these applications. Unfortunately, mechanical property data for braided composites do not appear extensively in the literature. Data are presented in this paper on the mechanical characterization of 2D triaxial braid, 2D triaxial braid plus stitching, and 3D (through-the-thickness) braid composite materials. The braided preforms all had the same graphite tow size and the same nominal braid architectures, (+/- 30 deg/0 deg), and were resin transfer molded (RTM) using the same mold for each of two different resin systems. Static data are presented for notched and unnotched tension, notched and unnotched compression, and compression after impact strengths at room temperature. In addition, some static results, after environmental conditioning, are included. Baseline tension and compression fatigue results are also presented, but only for the 3D braided composite material with one of the resin systems.

  6. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2004-03-01

    This technical progress report describes work performed from September 1, 2003, through February 29, 2004, for the project, ''Conformance Improvement Using Gels.'' We examined the properties of several ''partially formed'' gels that were formulated with a combination of high and low molecular weight HPAM polymers. After placement in 4-mm-wide fractures, these gels required about 25 psi/ft for brine to breach the gel (the best performance to date in fractures this wide). After this breach, stabilized residual resistance factors decreased significantly with increased flow rate. Also, residual resistance factors were up to 9 times greater for water than for oil. Nevertheless, permeability reduction factors were substantial for both water and oil flow. Gel with 2.5% chopped fiberglass effectively plugged 4-mm-wide fractures if a 0.5-mm-wide constriction was present. The ability to screen-out at a constriction appears crucial for particulate incorporation to be useful in plugging fractures. In addition to fiberglass, we examined incorporation of polypropylene fibers into gels. Once dispersed in brine or gelant, the polypropylene fibers exhibited the least gravity segregation of any particulate that we have tested to date. In fractures with widths of at least 2 mm, 24-hr-old gels (0.5% high molecular weight HPAM) with 0.5% fiber did not exhibit progressive plugging during placement and showed extrusion pressure gradients similar to those of gels without the fiber. The presence of the fiber roughly doubled the gel's resistance to first breach by brine flow. The breaching pressure gradients were not as large as for gels made with high and low molecular weight polymers (mentioned above). However, their material requirements and costs (i.e., polymer and/or particulate concentrations) were substantially lower than for those gels. A partially formed gel made with 0.5% HPAM did not enter a 0.052-mm-wide fracture when applying a pressure gradient of 65 psi/ft. This result

  7. Modeling chemoresponsive polymer gels.

    PubMed

    Kuksenok, Olga; Deb, Debabrata; Dayal, Pratyush; Balazs, Anna C

    2014-01-01

    Stimuli-responsive gels are vital components in the next generation of smart devices, which can sense and dynamically respond to changes in the local environment and thereby exhibit more autonomous functionality. We describe recently developed computational methods for simulating the properties of such stimuli-responsive gels in the presence of optical, chemical, and thermal gradients. Using these models, we determine how to harness light to drive shape changes and directed motion in spirobenzopyran-containing gels. Focusing on oscillating gels undergoing the Belousov-Zhabotinksy reaction, we demonstrate that these materials can spontaneously form self-rotating assemblies, or pinwheels. Finally, we model temperature-sensitive gels that encompass chemically reactive filaments to optimize the performance of this system as a homeostatic device for regulating temperature. These studies could facilitate the development of soft robots that autonomously interconvert chemical and mechanical energy and thus perform vital functions without the continuous need of external power sources. PMID:24498954

  8. In situ fabrication of ionic polyacrylamide-based preconcentrator on a simple poly(methyl methacrylate) microfluidic chip for capillary electrophoresis of anionic compounds.

    PubMed

    Yamamoto, Sachio; Hirakawa, Shingo; Suzuki, Shigeo

    2008-11-01

    A simple and efficient method was developed for fabrication of an anionic sample preconcentrator on a channel of a commercial poly(methyl methacrylate) (PMMA)-made microchip using no photolithography or etching technique. The originality of our preconcentrator is based on simple photochemical copolymerization of monomers using the following procedure: All channels of the PMMA-made microchip were filled with gel solution comprising acrylamide, N,N'-methylene-bisacrylamide, and 2-acrylamide-2-methylpropanesulfonic acid with riboflavin as a photocatalytic initiator. In situ polymerization near the cross of the sample outlet channel was performed by irradiation with an argon ion laser beam, which is also used as the light source for fluorometric detection. The electrokinetic property and electric repulsion between sample components and anionic groups on the polyacrylamide gel layer produce, trap, and concentrate anions within a few minutes at the interface of the cathodic side of the gel layer. This method displays concentration factors as high as 10 (5). The availability of ionic preconcentrator was demonstrated by applying sensitive analysis of oligosaccharides labeled with 8-aminopyrene-1,3,6-trisulfonate and some glycoproteins labeled with fluorescein isothiocyanate under various buffer systems. PMID:18841941

  9. Differential Cytochrome P450 2D Metabolism Alters Tafenoquine Pharmacokinetics

    PubMed Central

    Vuong, Chau; Xie, Lisa H.; Potter, Brittney M. J.; Zhang, Jing; Zhang, Ping; Duan, Dehui; Nolan, Christina K.; Sciotti, Richard J.; Zottig, Victor E.; Nanayakkara, N. P. Dhammika; Tekwani, Babu L.; Walker, Larry A.; Smith, Philip L.; Paris, Robert M.; Read, Lisa T.; Li, Qigui; Pybus, Brandon S.; Sousa, Jason C.; Reichard, Gregory A.; Smith, Bryan

    2015-01-01

    Cytochrome P450 (CYP) 2D metabolism is required for the liver-stage antimalarial efficacy of the 8-aminoquinoline molecule tafenoquine in mice. This could be problematic for Plasmodium vivax radical cure, as the human CYP 2D ortholog (2D6) is highly polymorphic. Diminished CYP 2D6 enzyme activity, as in the poor-metabolizer phenotype, could compromise radical curative efficacy in humans. Despite the importance of CYP 2D metabolism for tafenoquine liver-stage efficacy, the exact role that CYP 2D metabolism plays in the metabolism and pharmacokinetics of tafenoquine and other 8-aminoquinoline molecules has not been extensively studied. In this study, a series of tafenoquine pharmacokinetic experiments were conducted in mice with different CYP 2D metabolism statuses, including wild-type (WT) (reflecting extensive metabolizers for CYP 2D6 substrates) and CYPmouse 2D knockout (KO) (reflecting poor metabolizers for CYP 2D6 substrates) mice. Plasma and liver pharmacokinetic profiles from a single 20-mg/kg of body weight dose of tafenoquine differed between the strains; however, the differences were less striking than previous results obtained for primaquine in the same model. Additionally, the presence of a 5,6-ortho-quinone tafenoquine metabolite was examined in both mouse strains. The 5,6-ortho-quinone species of tafenoquine was observed, and concentrations of the metabolite were highest in the WT extensive-metabolizer phenotype. Altogether, this study indicates that CYP 2D metabolism in mice affects tafenoquine pharmacokinetics and could have implications for human tafenoquine pharmacokinetics in polymorphic CYP 2D6 human populations. PMID:25870069

  10. A Geometric Boolean Library for 2D Objects

    2006-01-05

    The 2D Boolean Library is a collection of C++ classes -- which primarily represent 2D geometric data and relationships, and routines -- which contain algorithms for 2D geometric Boolean operations and utility functions. Classes are provided for 2D points, lines, arcs, edgeuses, loops, surfaces and mask sets. Routines are provided that incorporate the Boolean operations Union(OR), XOR, Intersection and Difference. Various analytical geometry routines and routines for importing and exporting the data in various filemore » formats, are also provided in the library.« less

  11. A Geometric Boolean Library for 2D Objects

    SciTech Connect

    McBride, Corey L.; Yarberry, Victor; Jorgensen, Craig

    2006-01-05

    The 2D Boolean Library is a collection of C++ classes -- which primarily represent 2D geometric data and relationships, and routines -- which contain algorithms for 2D geometric Boolean operations and utility functions. Classes are provided for 2D points, lines, arcs, edgeuses, loops, surfaces and mask sets. Routines are provided that incorporate the Boolean operations Union(OR), XOR, Intersection and Difference. Various analytical geometry routines and routines for importing and exporting the data in various file formats, are also provided in the library.

  12. Polyacrylamide hydrogels: an effective tool for delivering liquid baits to pest ants (Hymenoptera: Formicidae).

    PubMed

    Buczkowski, Grzegorz; Roper, Elray; Chin, Darren

    2014-04-01

    Ant management in urban and natural areas often relies on toxic baits. Liquid baits are highly attractive to pest ants because they mimic natural food sources such as honeydew and nectar, the principal dietary components of many ants. However, liquid bait use has been limited owing to the lack of bait dispensers that are effective, inexpensive, and easy to service. The current study evaluated the potential of water-storing crystals (polyacrylamide spheres) to effectively deliver liquid thiamethoxam baits to laboratory colonies of Argentine ants, Linepithema humile Mayr. Results of laboratory trials show that bait crystals saturated in 25% sucrose solution containing 0.007% thiamethoxam are highly attractive to Argentine ants and highly effective against all castes and life stages, including workers, queens, and brood. Fresh bait crystals were highly effective and required approximately 2 d to kill all workers and approximately 6 d to achieve complete mortality in queens and brood. Results of bait aging tests show that the crystals lose approximately 70% of moisture in 8 h and the duration of outdoor exposure has a significant effect on moisture loss and subsequently bait acceptance and bait efficacy. A gradual decrease in mortality was observed for all castes and life stages as bait age increased. In general, fresh baits and those aged for < 8 h retained their efficacy and caused substantial mortality. Baits aged longer than 8 h were substantially less attractive and less effective. Horizontal transfer tests examined the transfer of thiamethoxam from live treated donors to live untreated recipients. The results show that donor ants that obtain thiamethoxam by feeding on bait crystals effectively transfer it to untreated recipient ants. The level of secondary mortality depended on the donor:recipient ratio, with approximately 40% recipient worker mortality with the 1:5 ratio and 15% recipient worker mortality with 1:10 or 1:20 ratios. However, no queens died in any

  13. Solids and nutrient removal from flushed swine manure using polyacrylamides

    SciTech Connect

    Vanotti, M.B.; Hunt, P.G.

    1999-12-01

    Most of the organic nutrients and reduced carbon (C) materials in liquid swine manure are contained in fine suspended particles that are not separated by available mechanical separators. Treatment with polyacrylamide (PAM) polymers prior to mechanical removal or gravity settling has the potential for enhancing solids-liquid separation, thus concentrating nitrogen (N), phosphorus (P), and organic C. In this work, the authors determined PAM charge and density characteristics most desirable for swine wastewater applications and established the optimum chemical requirement. Treatments were applied to flushed manure from two swine operations in North Carolina. Cationic PAMs significantly increased solids separation while performance of neutral and anionic types was not different from a control. Cationic PAMs with moderate-charge density (20%) were more effective than polymers with higher charge density. Flocs were large and effectively retained with a 1-mm screen. Optimum PAM rate varied with the amount of total suspended solids (TSS) in the liquid manure; 26 and 79 mg PAM/L for samples containing 1.5 and 4.1 g TSS/L, respectively. Corresponding TSS removal efficiencies were 90 to 94%. In contrast, screening without PAM treatment captured only 5 to 14% of the suspended solids. Polymer usage rate was consistent and averaged 2.0{degree} based on weight of dry solids produced. Volatile suspended solids (VSS) were highly correlated with TSS and comprised 79.5% of TSS. Chemical oxygen demand (COD) and organic nutrient concentrations in the effluent were also significantly decreased by PAM treatment. The decrease of COD concentration, an important consideration for odor control, was linearly related with removal of suspended solids, at a rate of 2.0 g COD/g TSS and 2.6 g COD/g VSS. Removal efficiency of organic N and P followed approximately a 1:1 relationship with removal efficiency of TSS. Chemical cost to capture 90% of the suspended solids was estimated to be $0.026 per

  14. AnisWave2D: User's Guide to the 2d Anisotropic Finite-DifferenceCode

    SciTech Connect

    Toomey, Aoife

    2005-01-06

    This document describes a parallel finite-difference code for modeling wave propagation in 2D, fully anisotropic materials. The code utilizes a mesh refinement scheme to improve computational efficiency. Mesh refinement allows the grid spacing to be tailored to the velocity model, so that fine grid spacing can be used in low velocity zones where the seismic wavelength is short, and coarse grid spacing can be used in zones with higher material velocities. Over-sampling of the seismic wavefield in high velocity zones is therefore avoided. The code has been implemented to run in parallel over multiple processors and allows large-scale models and models with large velocity contrasts to be simulated with ease.

  15. Klassifikation von Standardebenen in der 2D-Echokardiographie mittels 2D-3D-Bildregistrierung

    NASA Astrophysics Data System (ADS)

    Bergmeir, Christoph; Subramanian, Navneeth

    Zum Zweck der Entwicklung eines Systems, das einen unerfahrenen Anwender von Ultraschall (US) zur Aufnahme relevanter anatomischer Strukturen leitet, untersuchen wir die Machbarkeit von 2D-US zu 3D-CT Registrierung. Wir verwenden US-Aufnahmen von Standardebenen des Herzens, welche zu einem 3D-CT-Modell registriert werden. Unser Algorithmus unterzieht sowohl die US-Bilder als auch den CT-Datensatz Vorverarbeitungsschritten, welche die Daten durch Segmentierung auf wesentliche Informationen in Form von Labein für Muskel und Blut reduzieren. Anschließend werden diese Label zur Registrierung mittels der Match-Cardinality-Metrik genutzt. Durch mehrmaliges Registrieren mit verschiedenen Initialisierungen ermitteln wir die im US-Bild sichtbare Standardebene. Wir evaluierten die Methode auf sieben US-Bildern von Standardebenen. Fünf davon wurden korrekt zugeordnet.

  16. 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.

  17. 2D exchange 31P NMR spectroscopy of bacteriophage M13 and tobacco mosaic virus.

    PubMed Central

    Magusin, P C; Hemminga, M A

    1995-01-01

    Two-dimensional (2D) exchange 31P nuclear magnetic resonance spectroscopy is used to study the slow overall motion of the rod-shaped viruses M13 and tobacco mosaic virus in concentrated gels. Even for short mixing times, observed diagonal spectra differ remarkably from projection spectra and one-dimensional spectra. Our model readily explains this to be a consequence of the T2e anisotropy caused by slow overall rotation of the viruses about their length axis. 2D exchange spectra recorded for 30% (w/w) tobacco mosaic virus with mixing times < 1 s do not show any off-diagonal broadening, indicating that its overall motion occurs in the sub-Hz frequency range. In contrast, the exchange spectra obtained for 30% M13 show significant off-diagonal intensity for mixing times of 0.01 s and higher. A log-gaussian distribution around 25 Hz of overall diffusion coefficients mainly spread between 1 and 10(3) Hz faithfully reproduces the 2D exchange spectra of 30% M13 recorded at various mixing times in a consistent way. A small but notable change in diagonal spectra at increasing mixing time is not well accounted for by our model and is probably caused by 31P spin diffusion. PMID:7756532

  18. 2D-DIGE proteomic analysis identifies new potential therapeutic targets for adrenocortical carcinoma

    PubMed Central

    Armignacco, Roberta; Ercolino, Tonino; Canu, Letizia; Baroni, Gianna; Nesi, Gabriella; Galli, Andrea; Mannelli, Massimo; Luconi, Michaela

    2015-01-01

    Adrenocortical carcinoma (ACC) is a rare aggressive tumor with poor prognosis when metastatic at diagnosis. The tumor biology is still mostly unclear, justifying the limited specificity and efficacy of the anti-cancer drugs currently available. This study reports the first proteomic analysis of ACC by using two-dimensional-differential-in-gel-electrophoresis (2D-DIGE) to evaluate a differential protein expression profile between adrenocortical carcinoma and normal adrenal. Mass spectrometry, associated with 2D-DIGE analysis of carcinomas and normal adrenals, identified 22 proteins in 27 differentially expressed 2D spots, mostly overexpressed in ACC. Gene ontology analysis revealed that most of the proteins concurs towards a metabolic shift, called the Warburg effect, in adrenocortical cancer. The differential expression was validated by Western blot for Aldehyde-dehydrogenase-6-A1,Transferrin, Fascin-1,Lamin A/C,Adenylate-cyclase-associated-protein-1 and Ferredoxin-reductase. Moreover, immunohistochemistry performed on paraffin-embedded ACC and normal adrenal specimens confirmed marked positive staining for all 6 proteins diffusely expressed by neoplastic cells, compared with normal adrenal cortex. In conclusion, our preliminary findings reveal a different proteomic profile in adrenocortical carcinoma compared with normal adrenal cortex characterized by overexpression of mainly metabolic enzymes, thus suggesting the Warburg effect also occurs in ACC. These proteins may represent promising novel ACC biomarkers and potential therapeutic targets if validated in larger cohorts of patients. PMID:25691058

  19. Functional characterization of CYP2D6 enhancer polymorphisms

    PubMed Central

    Wang, Danxin; Papp, Audrey C.; Sun, Xiaochun

    2015-01-01

    CYP2D6 metabolizes nearly 25% of clinically used drugs. Genetic polymorphisms cause large inter-individual variability in CYP2D6 enzyme activity and are currently used as biomarker to predict CYP2D6 metabolizer phenotype. Previously, we had identified a region 115 kb downstream of CYP2D6 as enhancer for CYP2D6, containing two completely linked single nucleotide polymorphisms (SNPs), rs133333 and rs5758550, associated with enhanced transcription. However, the enhancer effect on CYP2D6 expression, and the causative variant, remained to be ascertained. To characterize the CYP2D6 enhancer element, we applied chromatin conformation capture combined with the next-generation sequencing (4C assays) and chromatin immunoprecipitation with P300 antibody, in HepG2 and human primary culture hepatocytes. The results confirmed the role of the previously identified enhancer region in CYP2D6 expression, expanding the number of candidate variants to three highly linked SNPs (rs133333, rs5758550 and rs4822082). Among these, only rs5758550 demonstrated regulating enhancer activity in a reporter gene assay. Use of clustered regularly interspaced short palindromic repeats mediated genome editing in HepG2 cells targeting suspected enhancer regions decreased CYP2D6 mRNA expression by 70%, only upon deletion of the rs5758550 region. These results demonstrate robust effects of both the enhancer element and SNP rs5758550 on CYP2D6 expression, supporting consideration of rs5758550 for CYP2D6 genotyping panels to yield more accurate phenotype prediction. PMID:25381333

  20. An Incompressible 2D Didactic Model with Singularity and Explicit Solutions of the 2D Boussinesq Equations

    NASA Astrophysics Data System (ADS)

    Chae, Dongho; Constantin, Peter; Wu, Jiahong

    2014-09-01

    We give an example of a well posed, finite energy, 2D incompressible active scalar equation with the same scaling as the surface quasi-geostrophic equation and prove that it can produce finite time singularities. In spite of its simplicity, this seems to be the first such example. Further, we construct explicit solutions of the 2D Boussinesq equations whose gradients grow exponentially in time for all time. In addition, we introduce a variant of the 2D Boussinesq equations which is perhaps a more faithful companion of the 3D axisymmetric Euler equations than the usual 2D Boussinesq equations.

  1. [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

  2. Efficient Visible Quasi-2D Perovskite Light-Emitting Diodes.

    PubMed

    Byun, Jinwoo; Cho, Himchan; Wolf, Christoph; Jang, Mi; Sadhanala, Aditya; Friend, Richard H; Yang, Hoichang; Lee, Tae-Woo

    2016-09-01

    Efficient quasi-2D-structure perovskite light-emitting diodes (4.90 cd A(-1) ) are demonstrated by mixing a 3D-structured perovskite material (methyl ammonium lead bromide) and a 2D-structured perovskite material (phenylethyl ammonium lead bromide), which can be ascribed to better film uniformity, enhanced exciton confinement, and reduced trap density. PMID:27334788

  3. Integrating Mobile Multimedia into Textbooks: 2D Barcodes

    ERIC Educational Resources Information Center

    Uluyol, Celebi; Agca, R. Kagan

    2012-01-01

    The major goal of this study was to empirically compare text-plus-mobile phone learning using an integrated 2D barcode tag in a printed text with three other conditions described in multimedia learning theory. The method examined in the study involved modifications of the instructional material such that: a 2D barcode was used near the text, the…

  4. Nonlinear Strain Stiffening Is Not Sufficient to Explain How Far Cells Can Feel on Fibrous Protein Gels

    PubMed Central

    Rudnicki, Mathilda S.; Cirka, Heather A.; Aghvami, Maziar; Sander, Edward A.; Wen, Qi; Billiar, Kristen L.

    2013-01-01

    Recent observations suggest that cells on fibrous extracellular matrix materials sense mechanical signals over much larger distances than they do on linearly elastic synthetic materials. In this work, we systematically investigate the distance fibroblasts can sense a rigid boundary through fibrous gels by quantifying the spread areas of human lung fibroblasts and 3T3 fibroblasts cultured on sloped collagen and fibrin gels. The cell areas gradually decrease as gel thickness increases from 0 to 150 μm, with characteristic sensing distances of >65 μm below fibrin and collagen gels, and spreading affected on gels as thick as 150 μm. These results demonstrate that fibroblasts sense deeper into collagen and fibrin gels than they do into polyacrylamide gels, with the latter exhibiting characteristic sensing distances of <5 μm. We apply finite-element analysis to explore the role of strain stiffening, a characteristic mechanical property of collagen and fibrin that is not observed in polyacrylamide, in facilitating mechanosensing over long distances. Our analysis shows that the effective stiffness of both linear and nonlinear materials sharply increases once the thickness is reduced below 5 μm, with only a slight enhancement in sensitivity to depth for the nonlinear material at very low thickness and high applied traction. Multiscale simulations with a simplified geometry predict changes in fiber alignment deep into the gel and a large increase in effective stiffness with a decrease in substrate thickness that is not predicted by nonlinear elasticity. These results suggest that the observed cell-spreading response to gel thickness is not explained by the nonlinear strain-stiffening behavior of the material alone and is likely due to the fibrous nature of the proteins. PMID:23823219

  5. Van der Waals stacked 2D layered materials for optoelectronics

    NASA Astrophysics Data System (ADS)

    Zhang, Wenjing; Wang, Qixing; Chen, Yu; Wang, Zhuo; Wee, Andrew T. S.

    2016-06-01

    The band gaps of many atomically thin 2D layered materials such as graphene, black phosphorus, monolayer semiconducting transition metal dichalcogenides and hBN range from 0 to 6 eV. These isolated atomic planes can be reassembled into hybrid heterostructures made layer by layer in a precisely chosen sequence. Thus, the electronic properties of 2D materials can be engineered by van der Waals stacking, and the interlayer coupling can be tuned, which opens up avenues for creating new material systems with rich functionalities and novel physical properties. Early studies suggest that van der Waals stacked 2D materials work exceptionally well, dramatically enriching the optoelectronics applications of 2D materials. Here we review recent progress in van der Waals stacked 2D materials, and discuss their potential applications in optoelectronics.

  6. Unitary quantum lattice gas representation of 2D quantum turbulence

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Vahala, George; Vahala, Linda; Soe, Min

    2011-05-01

    Quantum vortex structures and energy cascades are examined for two dimensional quantum turbulence (2D QT) using a special unitary evolution algorithm. The qubit lattice gas (QLG) algorithm, is employed to simulate the weakly-coupled Bose-Einstein condensate (BEC) governed by the Gross-Pitaevskii (GP) equation. A parameter regime is uncovered in which, as in 3D QT, there is a very short Poincare recurrence time. This short recurrence time is destroyed as the nonlinear interaction energy is increased. Energy cascades for 2D QT are considered to examine whether 2D QT exhibits the inverse cascades of 2D classical turbulence. In the parameter regime considered, the spectra analysis reveals no such dual cascades---dual cascades being a hallmark of 2D classical turbulence.

  7. CYP2D6 polymorphism in patients with eating disorders.

    PubMed

    Peñas-Lledó, E M; Dorado, P; Agüera, Z; Gratacós, M; Estivill, X; Fernández-Aranda, F; Llerena, A

    2012-04-01

    CYP2D6 polymorphism is associated with variability in drug response, endogenous metabolism (that is, serotonin), personality, neurocognition and psychopathology. The relationship between CYP2D6 genetic polymorphism and the risk of eating disorders (ED) was analyzed in 267 patients with ED and in 285 controls. A difference in the CYP2D6 active allele distribution was found between these groups. Women carrying more than two active genes (ultrarapid metabolizers) (7.5 vs 4.6%) or two (67 vs 58.9%) active genes were more frequent among patients with ED, whereas those with one (20.6 vs 30.2%) or zero active genes (4.9 vs 6.3%) were more frequent among controls (P<0.05). Although further research is needed, present findings suggest an association between CYP2D6 and ED. CYP2D6 allele distribution in patients with ED seems related to increased enzyme activity. PMID:20877302

  8. 2D materials and van der Waals heterostructures.

    PubMed

    Novoselov, K S; Mishchenko, A; Carvalho, A; Castro Neto, A H

    2016-07-29

    The physics of two-dimensional (2D) materials and heterostructures based on such crystals has been developing extremely fast. With these new materials, truly 2D physics has begun to appear (for instance, the absence of long-range order, 2D excitons, commensurate-incommensurate transition, etc.). Novel heterostructure devices--such as tunneling transistors, resonant tunneling diodes, and light-emitting diodes--are also starting to emerge. Composed from individual 2D crystals, such devices use the properties of those materials to create functionalities that are not accessible in other heterostructures. Here we review the properties of novel 2D crystals and examine how their properties are used in new heterostructure devices. PMID:27471306

  9. In-phantom dosimetry for BNCT with Fricke and normoxic-polymer gels

    NASA Astrophysics Data System (ADS)

    Gambarini, G.; Agosteo, S.; Carrara, M.; Gay, S.; Mariani, M.; Pirola, L.; Vanossi, E.

    2006-05-01

    Measurements of in-phantom dose distributions and images are important for Boron Neutron Capture Therapy treatment planning. The method for spatial determination of absorbed doses in thermal or epithermal neutron fields, based on Fricke-xylenol-orange-infused gel dosimeters in form of layers, has revealed to be very reliable, as gel layer dosimeters give the possibility of obtaining spatial dose distributions and measurements of each dose contribution in neutron fields, by means of a properly studied procedure. Quite recently, BNCT has been applied to treat liver metastases; in this work the results of in-phantom dosimetry for explanted liver in BNCT treatments are described. Moreover, polyacrylamide gel (PAG) dosimeters in which a polymerization process appears as a consequence of absorbed dose, have been recently tested, because of their characteristic absence of diffusion. In fact, due to the diffusion of ferric ions, Fricke-gel dosimeters require prompt analysis after exposure to avoid spatial information loss. In this work the preliminary results of a study about the reliability of polymer gel in BNCT dosimetry are also discussed. Gel layers have been irradiated in a phantom exposed in the thermal column of the TRIGA MARK II reactor (Pavia). The results obtained with the two kinds of gel dosimeter have been compared.

  10. Viscoelasticity of silica gels

    SciTech Connect

    Scherer, G.W.

    1995-12-01

    The response of silica gels to mechanical loads depends on the properties of the solid phase and the permeability of the network. Understanding this behavior is essential for modeling of stresses developed during drying or heating of gels. The permeability and the mechanical properties are readily determined from a simple beam-bending experiment, by measuring the load relaxation that occurs at constant deflection. Load decay results from movement of the liquid within the network; in addition, there may be viscoelastic relaxation of the network itself. Silica gel is viscoelastic in chemically aggressive media, but in inert liquids (such as ethanol or acetone) it is elastic. Experiments show that the viscoelastic relaxation time decreases as the concentration and pH of the water in the pore liquid increase. During drying, the permeability decreases and the viscosity increases, both exhibiting a power-law dependence on density of the gel network.

  11. Testosterone Nasal Gel

    MedlinePlus

    ... enough natural testosterone). Testosterone nasal gel is used only for men with low testosterone levels caused by ... is a controlled substance. Prescriptions may be refilled only a limited number of times; ask your pharmacist ...

  12. Microfluidics with Gel Emulsions

    NASA Astrophysics Data System (ADS)

    Priest, Craig; Surenjav, Enkhtuul; Herminghaus, Stephan; Seemann, Ralf

    2006-03-01

    Microfluidic processing is usually achieved using single phase liquids. Instead, we use monodisperse emulsions to compartment liquids within microchannel geometries. At low continuous phase volume fractions, droplets self-organize to form well-defined arrangements, analogous to foam. While it is well-known that confined geometries can induce rearrangement of foam compartments at the millimeter-scale, similar dynamics are also expected for gel emulsions. We have studied online generation, organization and manipulation of gel emulsions using a variety of microchannel geometries. ``Passive'' reorganization, based on fixed channel geometries, can be supplemented by ``active'' manipulation by incorporating a ferrofluid phase. A ferromagnetic phase facilitates reorganization of liquid compartments on demand using an electromagnetic trigger. Moreover, coalescence between adjacent compartments within a gel emulsion can be induced using electrical potential. Microfluidics using gel emulsions will be well-suited for combinatorial chemistry, DNA sequencing, drug screening and protein crystallizations.

  13. Preparation of chitosan gel

    NASA Astrophysics Data System (ADS)

    Moussaoui, Y.; Mnasri, N.; Elaloui, E.; Ben Salem, R.; Lagerge, S.; de Menorval, L. C.

    2012-06-01

    Aerogel conditioning of the chitosan makes it possible to prepare porous solids of significant specific surface. The increase in the chitosan concentration or the degree of acetylation decreases the specific surface of the synthesized chitosan gel. Whereas drying with supercritical CO2 more effectively makes it possible to preserve the volume of the spheres of gel and to have a more significant specific surface in comparison with evaporative drying.

  14. 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

  15. Conformance Improvement Using Gels

    SciTech Connect

    Seright, Randall S.; Schrader, Richard; II Hagstrom, John; Wang, Ying; Al-Dahfeeri, Abdullah; Gary, Raven; Marin; Amaury; Lindquist, Brent

    2002-09-26

    This research project had two objectives. The first objective was 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 was to optimize treatments in fractured production wells, where the gel must reduce permeability to water much more than that to oil.

  16. Janus Gel Fabrication Using Liquid Drop Coalescence and Limited Mixing in the Hele-Shaw Geometry

    NASA Astrophysics Data System (ADS)

    Gonzalez, Brittany; Moran, Alexis; Lee, Donghee; Ryu, Sangjin

    2015-11-01

    Hydrogel substrates of tunable stiffness have been actively utilized for in vitro cell mechanobiology study. Here we present a new method to fabricate Janus polyacrylamide gel based on limited mixing between liquid drops coalescing in the Hele-Shaw geometry. Two pre-polymer drops with different concentrations were sandwiched and squeezed between two parallel glass surfaces. Once the drops coalesced in the decreased gap between the surfaces, gelation was initiated by UV light exposure with various time delays. AFM nano-indentation was utilized to map the Young's modulus of obtained gels. Fabricated Janus gels had two regions of different Young's moduli interfaced by the stiffness gradient zone, and the width of the gradient zone increased with the delay time. We acknowledge support from Bioengineering for Human Health grant from UNL and UNMC, and NSF REU grant for UNL.

  17. Detection and characterization of heparin-binding proteins with a gel overlay procedure

    SciTech Connect

    Mehlman, T.; Burgess, W.H. )

    1990-07-01

    The binding of {sup 125}I-labeled derivatives of heparin has been used by several investigators to identify heparin-binding fragments of different heparin-binding proteins. In this report we utilize the procedure described by J.W. Smith and D.J. Knauer (1987, Anal. Biochem. 160, 105-114) to produce {sup 125}I-fluorescein-heparin. Using this derivative, we compare the use of gel overlay procedures with Western blot procedures for the detection of heparin-binding proteins following polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. We show that the gel overlay procedure is a relatively simple and sensitive method for visualizing heparin-binding proteins. In addition, we use the procedure to characterize the heparin-binding properties of heparin-binding growth factor 1 (acidic fibroblast growth factor) with synthetic peptide competitors and site-directed mutants of the growth factor.

  18. Previsible silver staining of protein in electrophoresis gels with mass spectrometry compatibility.

    PubMed

    Jin, Li-Tai; Li, Xiao-Kun; Cong, Wei-Tao; Hwang, Sun-Young; Choi, Jung-Kap

    2008-12-15

    A convenient silver staining method for protein in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels is described. The method is previsible, sensitive, and mass spectrometry (MS) compatible. Two visible counter ion dyes, ethyl violet (EV) and zincon (ZC), were used in the first staining solution with a detection limit of 2 to 8 ng/band in approximately 1h. The dye-stained gel can be further stained by silver staining, which is based on acidic silver staining employing ZC with sodium thiosulfate as silver ion sensitizers. Especially, ZC has silver ion reducing power by cleavage of the diazo bond of the dye during silver reduction. The second silver staining can be completed in approximately 1h with a detection limit of 0.2 ng/band. PMID:18804088

  19. Polyacrylamide films as a tool for investigating qualitative and quanitative aspects of the staining of glycosaminoglycans with basic dyes.

    PubMed

    Tas, J

    1977-05-01

    With the introduction of model films of polyacrylamide gel into which purified glycosaminogly cans (GAGs) have been 'incorporated', the direct recording of metachromatic spectra with virtually no interference of the corresponding orthochromatic peaks has become possible. Because this model system yields situations comparable to those of stained sections under the microscope, it is well suited for investigating qualitative and quantitative aspects of histochemical staining procedures. Previous model experiments have shown that under aqueous conditions only minor differences can be observed between the metachromatic peaks of different GAGs complexed with a suitable dye (e.g. Toluidine Blue O, Thionin, Safranin O, Cresyl Violet, Cystal Violet). In non-aqueous media, such as glycerol and ethylene glycol, the complexes with Toluidine Blue O revealed a special pattern for heparin, having a metachromatic peak (517 nm) about 30 nm lower than that of all other GAGs. This observation has formed the basis of a method for the qualitative microspectrophotometric detection of heparin in situ which was worked out by combining model film experiments with microspectrophotometric data obtained from rat mast cells. Since only a limited number of cells in necessary for obtaining reliable data with this method, the presence of heparin in the cytoplasmic granules of normal human mast cells and basophilic granulocytes could thus be proved directly. Alcian Blue 8GX, another basic dye frequently use in GAG histochemistry, has also been investigated with polyacrylamide films. In contrast to the metachromatic dyes, the rate of staining with Alcian Blue depends to a large extent on the rate of penetration of the dye into the model films. The rate of penetration is also a phenomenon of great importance for dye binding in situ, where complex basic protein molecules may form a barrier for the Alcian Blue molecules. The model film studies performed so far have yielded conditions that provide

  20. Targeted fluorescence imaging enhanced by 2D materials: a comparison between 2D MoS2 and graphene oxide.

    PubMed

    Xie, Donghao; Ji, Ding-Kun; Zhang, Yue; Cao, Jun; Zheng, Hu; Liu, Lin; Zang, Yi; Li, Jia; Chen, Guo-Rong; James, Tony D; He, Xiao-Peng

    2016-08-01

    Here we demonstrate that 2D MoS2 can enhance the receptor-targeting and imaging ability of a fluorophore-labelled ligand. The 2D MoS2 has an enhanced working concentration range when compared with graphene oxide, resulting in the improved imaging of both cell and tissue samples. PMID:27378648