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

Serwer, Philip, E-mail: serwer@uthscsa.edu; Wright, Elena T.; Liu, Zheng

DNA packaging of phages phi29, T3 and T7 sometimes produces incompletely packaged DNA with quantized lengths, based on gel electrophoretic band formation. We discover here a packaging ATPase-free, in vitro model for packaged DNA length quantization. We use directed evolution to isolate a five-site T3 point mutant that hyper-produces tail-free capsids with mature DNA (heads). Three tail gene mutations, but no head gene mutations, are present. A variable-length DNA segment leaks from some mutant heads, based on DNase I-protection assay and electron microscopy. The protected DNA segment has quantized lengths, based on restriction endonuclease analysis: six sharp bands of DNAmore » missing 3.7–12.3% of the last end packaged. Native gel electrophoresis confirms quantized DNA expulsion and, after removal of external DNA, provides evidence that capsid radius is the quantization-ruler. Capsid-based DNA length quantization possibly evolved via selection for stalling that provides time for feedback control during DNA packaging and injection. - Graphical abstract: Highlights: • We implement directed evolution- and DNA-sequencing-based phage assembly genetics. • We purify stable, mutant phage heads with a partially leaked mature DNA molecule. • Native gels and DNase-protection show leaked DNA segments to have quantized lengths. • Native gels after DNase I-removal of leaked DNA reveal the capsids to vary in radius. • Thus, we hypothesize leaked DNA quantization via variably quantized capsid radius.« less

Charge Transfer Modulated Self-Assembly in Poly(aryl ether) Dendron Derivatives with Improved Stability and Transport Characteristics.

PubMed

Satapathy, Sitakanta; Prasad, Edamana

2016-10-05

Alteration of native gelation properties of anthracene and pyrene cored first generation poly(aryl ether) dendrons, G1-An and G1-Py, by introducing a common acceptor, 2,4,7-trinitro-9H-fluoren-9-one (TNF), results in forming charge transfer gels in long chain alcoholic solvents. This strategy leads to significant perturbation of optical and electronic properties within the gel matrix. Consequently, a noticeable increase of their electrical conductivities is observed, making these poly(aryl ether) dendron based gels potential candidates for organic electronics. While the dc-conductivity (σ) value for the native gel from G1-An is 2.8 × 10 -4 S m -1 , the value increased 3 times (σ = 8.7 × 10 -4 S m -1 ) for its corresponding charge transfer gel. Further, the dc-conductivity for the native gel self-assembled from G1-Py dramatically enhanced by approximately an order of magnitude from 4.9 × 10 -4 to 1.3 × 10 -3 S m -1 , under the influence of an acceptor. Apart from H-bonding and π···π interactions, charge transfer results in the formation of a robust 3D network of fibers, with improved aspect ratio, providing high thermo-mechanical stability to the gels compared to the native ones. The charge transfer gels self-assembled from G1-An/TNF (1:1) and G1-Py/TNF exhibit a 7.3- and 2.5-fold increase in their yield stress, respectively, compared to their native assemblies. A similar trend follows in the case of their thermal stabilities. This is attributed to the typical bilayer self-assembly of the former which is not present in the case of G1-Py/TNF charge transfer gel. Density functional calculations provide deeper insights accounting for the role of charge transfer interactions in the mode of self-assembly. The 1D potential energy surface for the G1-An/TNF dimer and G1-Py/TNF dimer is found to be 11.8 and 1.9 kcal mol -1 more stable than their corresponding native gel dimers, G1-An/G1-An and G1-Py/G1-Py, respectively.

CN-GELFrEE - Clear Native Gel-eluted Liquid Fraction Entrapment Electrophoresis

PubMed Central

Skinner, Owen S.; Do Vale, Luis H. F.; Catherman, Adam D.; Havugimana, Pierre C.; Valle de Sousa, Marcelo; Domont, Gilberto B.; Kelleher, Neil L.; Compton, Philip D.

2016-01-01

Protein complexes perform an array of crucial cellular functions. Elucidating their non-covalent interactions and dynamics is paramount for understanding the role of complexes in biological systems. While the direct characterization of biomolecular assemblies has become increasingly important in recent years, native fractionation techniques that are compatible with downstream analysis techniques, including mass spectrometry, are necessary to further expand these studies. Nevertheless, the field lacks a high-throughput, wide-range, high-recovery separation method for native protein assemblies. Here, we present clear native gel-eluted liquid fraction entrapment electrophoresis (CN-GELFrEE), which is a novel separation modality for non-covalent protein assemblies. CN-GELFrEE separation performance was demonstrated by fractionating complexes extracted from mouse heart. Fractions were collected over 2 hr and displayed discrete bands ranging from ~30 to 500 kDa. A consistent pattern of increasing molecular weight bandwidths was observed, each ranging ~100 kDa. Further, subsequent reanalysis of native fractions via SDS-PAGE showed molecular-weight shifts consistent with the denaturation of protein complexes. Therefore, CN-GELFrEE was proved to offer the ability to perform high-resolution and high-recovery native separations on protein complexes from a large molecular weight range, providing fractions that are compatible with downstream protein analyses. PMID:26967310

[Purification and properties of Se-containing allophycocyanins from selenium rich Spirulina platensis].

PubMed

Huang, Zhi; Yang, Fang; Zheng, Wen-Jie

2006-06-01

Three Se-containing allophycocyanins (Se-APC) with high purity were purified from Se rich Spirulina platensis (Se-sp.) by hydroxyapatite chromatography, DEAE-52 anion-exchange chromatography and native gel preparative electrophoresis. Their biochemicial properties were explored by spectral scanning and electrophoresis analysis of Native-PAGE, SDS-PAGE and IEF on thin slab gel. Protein molecular weight (MW) of APC aggregation was determined by gel filter on Sephadex G-200 column. Se content of native and denatured Se-APC was detected by 2, 3-DAN fluorocence method. According to visible and fluorescence spectral character, three purified fractions of APC were identified to be APCI, APCII and APCIII. Native-PAGE and SDS-PAGE analysis revealed that they all shaped trimer (alphabeta) 3 of alpha and beta subunit with molecular mass of 18.3kDa and 15.7kDa, whereas APCI contains gamma subunit (about 32kDa) visibly and APCIII maybe contain the linker peptide of L(C)(8 - 10 kDa) based on their MW to be determined of 130.9, 98.1 and 106.30 kDa. IEF detection showed that the pl of Se-APCs was 4.76, 4.85 and 5.02 respectively. Se content of three purified Se-APCs were 316, 273 and 408 microg/g, which decreased about 25% after deaggregation treatment by 0.50 mol/L NaSCN and decreased more than 50% after denaturation treatment by 2-mercaptoethanol and reached to a steady content of 132 microg/g on average. These results indicated that Se incorporation into APC had no influence on function of energy transfer as well as biochemical property of APCs, and Se binding with APCs was highly relevant to its aggregation states whereas Se integrated steadily with its subunits.

Analysis of metal-binding proteins separated by non-denaturating gel electrophoresis using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS).

PubMed

Becker, J Susanne; Mounicou, Sandra; Zoriy, Miroslav V; Becker, J Sabine; Lobinski, Ryszard

2008-09-15

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) have become established as very efficient and sensitive biopolymer and elemental mass spectrometric techniques for studying metal-binding proteins (metalloproteins) in life sciences. Protein complexes present in rat tissues (liver and kidney) were separated in their native state in the first dimension by blue native gel electrophoresis (BN-PAGE). Essential and toxic metals, such as zinc, copper, iron, nickel, chromium, cadmium and lead, were detected by scanning the gel bands using quadrupole LA-ICP-MS with and without collision cell as a microanalytical technique. Several proteins were identified by using MALDI-TOF-MS together with a database search. For example, on one protein band cut from the BN-PAGE gel and digested with the enzyme trypsin, two different proteins - protein FAM44B and cathepsin B precursor - were identified. By combining biomolecular and elemental mass spectrometry, it was possible to characterize and identify selected metal-binding rat liver and kidney tissue proteins.

Electrophoretic mobility shift in native gels indicates calcium-dependent structural changes of neuronal calcium sensor proteins.

PubMed

Viviano, Jeffrey; Krishnan, Anuradha; Wu, Hao; Venkataraman, Venkat

2016-02-01

In proteins of the neuronal calcium sensor (NCS) family, changes in structure as well as function are brought about by the binding of calcium. In this article, we demonstrate that these structural changes, solely due to calcium binding, can be assessed through electrophoresis in native gels. The results demonstrate that the NCS proteins undergo ligand-dependent conformational changes that are detectable in native gels as a gradual decrease in mobility with increasing calcium but not other tested divalent cations such as magnesium, strontium, and barium. Surprisingly, such a gradual change over the entire tested range is exhibited only by the NCS proteins but not by other tested calcium-binding proteins such as calmodulin and S100B, indicating that the change in mobility may be linked to a unique NCS family feature--the calcium-myristoyl switch. Even within the NCS family, the changes in mobility are characteristic of the protein, indicating that the technique is sensitive to the individual features of the protein. Thus, electrophoretic mobility on native gels provides a simple and elegant method to investigate calcium (small ligand)-induced structural changes at least in the superfamily of NCS proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

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

PubMed

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

2018-05-01

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

Partial Purification of a Megadalton DNA Replication Complex by Free Flow Electrophoresis.

PubMed

Li, Caroline M; Miao, Yunan; Lingeman, Robert G; Hickey, Robert J; Malkas, Linda H

2016-01-01

We describe a gentle and rapid method to purify the intact multiprotein DNA replication complex using free flow electrophoresis (FFE). In particular, we applied FFE to purify the human cell DNA synthesome, which is a multiprotein complex that is fully competent to carry-out all phases of the DNA replication process in vitro using a plasmid containing the simian virus 40 (SV40) origin of DNA replication and the viral large tumor antigen (T-antigen) protein. The isolated native DNA synthesome can be of use in studying the mechanism by which mammalian DNA replication is carried-out and how anti-cancer drugs disrupt the DNA replication or repair process. Partially purified extracts from HeLa cells were fractionated in a native, liquid based separation by FFE. Dot blot analysis showed co-elution of many proteins identified as part of the DNA synthesome, including proliferating cell nuclear antigen (PCNA), DNA topoisomerase I (topo I), DNA polymerase δ (Pol δ), DNA polymerase ɛ (Pol ɛ), replication protein A (RPA) and replication factor C (RFC). Previously identified DNA synthesome proteins co-eluted with T-antigen dependent and SV40 origin-specific DNA polymerase activity at the same FFE fractions. Native gels show a multiprotein PCNA containing complex migrating with an apparent relative mobility in the megadalton range. When PCNA containing bands were excised from the native gel, mass spectrometric sequencing analysis identified 23 known DNA synthesome associated proteins or protein subunits.

Pepsin diffusion in dairy gels depends on casein concentration and microstructure.

PubMed

Thévenot, J; Cauty, C; Legland, D; Dupont, D; Floury, J

2017-05-15

Fundamental knowledge of gastric digestion had only focused on acid diffusion from the gastric fluid, but no data are available for pepsin diffusion. Using fluorescence recovery after photobleaching technique, diffusion coefficients D of fluorescein isothiocyanate (FITC)-pepsin were measured in rennet gels across a range of casein concentrations allowing to form networks of protein aggregates with different structures. To investigate the microstructural parameters of native gels, electron microscopy image analysis were performed and qualitatively related to diffusion behavior of FITC-pepsin in these dairy gels. This study is the first report on quantification of pepsin diffusion in dairy product. Pepsin diffusion in rennet gels depends on casein concentration and microstructure. Models of polymer science can be used to assess D in dairy gel. Such data should be confronted with pepsin activity in acidic environment, and will be very useful as input parameters in mathematical models of food degradation in the human stomach. Copyright © 2016 Elsevier Ltd. All rights reserved.

Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 1. Preparation of more than 4000 native protein maps.

PubMed

Jin, Ya; Zhang, Jun; Yuan, Qi; Manabe, Takashi; Tan, Wen

2015-08-01

Soluble proteins of human bronchial smooth muscle cells (HBSMC) were separated by nondenaturing micro 2DE and a 30 mm × 40 mm area of the CBB-stained slab gel (1.0 mm thick) was cut into 1.1 mm × 1.1 mm squares, then the proteins in the 972 gel pieces (squares) were applied to quantitative LC-MS/MS. Grid-cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC-MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data [1]. Totally 4323 proteins were identified in successfully analyzed 967 squares and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The quantity of the proteins distributed from 3.6% to 1 × 10(-5) % of the total protein quantity in the grid area. Each protein map was characterized by several features, including the position of quantity peak square, number of detected squares, and degree of concentration (focused or dispersed). About 4% of the proteins were detected in 100 or more squares, suggesting that they might be ubiquitous and interacting with other proteins. In contrast, many proteins showed more concentrated quantity distribution and the quantity peak positions of 565 proteins with a defined degree of concentration were summarized into a quantity peak map. These results for the first time visualized the distribution patterns of cellular proteins on a nondenaturing 2D gel. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermostability of glucose oxidase in silica gel obtained by sol-gel method and in solution studied by fluorimetric method.

PubMed

Przybyt, Małgorzata; Miller, Ewa; Szreder, Tomasz

2011-04-04

The thermostability of glucose oxidase entrapped in silica gel obtained by sol-gel method was studied by thermostimulated fluorescence of FAD at pH 5 and 7 and compared with that of the native enzyme in the solution and at the presence of ethanol. The unfolding temperatures were found to be lower for the enzyme immobilised in gel as compared with the native enzyme but higher as for the enzyme at the presence of ethanol. In gel, the thermal denaturation of glucose oxidase is independent on pH while in solution the enzyme is more stable at pH 5. The investigation the enzyme in different environment by steady-state fluorescence of FAD and tryptophan, synchronous fluorescence and time-resolved fluorescence of tryptophan indicates that the state of the molecule (tertiary structure and molecular dynamics) is different in gel and in solution. The ethanol produced during gel precursor hydrolysis is not the main factor influencing the thermostability of the enzyme but more important are interactions of the protein with the gel lattice. Copyright © 2011 Elsevier B.V. All rights reserved.

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

PubMed

Robinson, Nicholas P

2013-01-01

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

Lipid, Detergent, and Coomassie Blue G-250 Affect the Migration of Small Membrane Proteins in Blue Native Gels

PubMed Central

Crichton, Paul G.; Harding, Marilyn; Ruprecht, Jonathan J.; Lee, Yang; Kunji, Edmund R. S.

2013-01-01

Blue native gel electrophoresis is a popular method for the determination of the oligomeric state of membrane proteins. Studies using this technique have reported that mitochondrial carriers are dimeric (composed of two ∼32-kDa monomers) and, in some cases, can form physiologically relevant associations with other proteins. Here, we have scrutinized the behavior of the yeast mitochondrial ADP/ATP carrier AAC3 in blue native gels. We find that the apparent mass of AAC3 varies in a detergent- and lipid-dependent manner (from ∼60 to ∼130 kDa) that is not related to changes in the oligomeric state of the protein, but reflects differences in the associated detergent-lipid micelle and Coomassie Blue G-250 used in this technique. Higher oligomeric state species are only observed under less favorable solubilization conditions, consistent with aggregation of the protein. Calibration with an artificial covalent AAC3 dimer indicates that the mass observed for solubilized AAC3 and other mitochondrial carriers corresponds to a monomer. Size exclusion chromatography of purified AAC3 in dodecyl maltoside under blue native gel-like conditions shows that the mass of the monomer is ∼120 kDa, but appears smaller on gels (∼60 kDa) due to the unusually high amount of bound negatively charged dye, which increases the electrophoretic mobility of the protein-detergent-dye micelle complex. Our results show that bound lipid, detergent, and Coomassie stain alter the behavior of mitochondrial carriers on gels, which is likely to be true for other small membrane proteins where the associated lipid-detergent micelle is large when compared with the mass of the protein. PMID:23744064

[Immobilization of pectawamorine G10x by gel entrapment].

PubMed

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

1979-01-01

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

Structural and thermo-rheological analysis of solutions and gels of a β-lactoglobulin fraction isolated from bovine whey.

PubMed

Estévez, Natalia; Fuciños, Pablo; Bargiela, Verónica; Pastrana, Lorenzo; Tovar, Clara Asunción; Luisa Rúa, M

2016-05-01

A β-Lactoglobulin fraction (r-βLg) was isolated from milk whey hydrolysates produced with cardosins from Cynara cardunculus. The impact of the technological process on the r-βLg structure and how in turn this determined its heat-induced gelation was investigated. Results were analysed taking pure β-Lg (p-βLg) as control sample. The process induced changes in the r-βLg native conformation causing exposure of hydrophobic groups, lower thermal stability and also, shorter thermal treatments needed to give rise to non-native and aggregated species. At pH 3.2, r-βLg and p-βLg solutions exhibited two gelation steps, with the advantage that r-βLg protein may form stable gels at lower temperature than p-βLg. At pH 7.2, a specific thermo-viscoelastic stability to 73 °C was found, which corresponded to the gel point in both protein solutions. The difference was that while for p-βLg solution in sol state δ<45° (solid-like), however for r-βLg solution δ>45° (fluid-like). Copyright © 2015 Elsevier Ltd. All rights reserved.

Automated in-line gel filtration for native state mass spectrometry.

PubMed

Waitt, Greg M; Xu, Robert; Wisely, G Bruce; Williams, Jon D

2008-02-01

Characterization of protein-ligand complexes by nondenaturing mass spectrometry provides direct evidence of drug-like molecules binding with potential therapeutic targets. Typically, protein-ligand complexes to be analyzed contain buffer salts, detergents, and other additives to enhance protein solubility, all of which make the sample unable to be analyzed directly by electrospray ionization mass spectrometry. This work describes an in-line gel-filtration method that has been automated and optimized. Automation was achieved using commercial HPLC equipment. Gel column parameters that were optimized include: column dimensions, flow rate, packing material type, particle size, and molecular weight cut-off. Under optimal conditions, desalted protein ions are detected 4 min after injection and the analysis is completed in 20 min. The gel column retains good performance even after >200 injections. A demonstration for using the in-line gel-filtration system is shown for monitoring the exchange of fatty acids from the pocket of a nuclear hormone receptor, peroxisome proliferator activator-delta (PPARdelta) with a tool compound. Additional utilities of in-line gel-filtration mass spectrometry system will also be discussed.

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

PubMed Central

2011-01-01

Background Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG) vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS) to characterize potential protein-protein interactions in membrane fractions. Results Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins), which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane helixes were identified well in our work. Conclusions In this study, we utilized LC-MS/MS in combination with blue native PAGE to characterize modular components of multiprotein complexes in BCG membrane fractions. The results demonstrated that the proteomic strategy was a reliable and reproducible tool for analysis of BCG multiprotein complexes. The identification in our study may provide some evidence for further study of BCG protein interaction. PMID:21241518

Synthesis, properties, and biomedical applications of gelatin methacryloyl (GelMA) hydrogels

PubMed Central

Yue, Kan; Santiago, Grissel Trujillo-de; Alvarez, Mario Moisés; Tamayol, Ali; Annabi, Nasim; Khademhosseini, Ali

2015-01-01

Gelatin methacryloyl (GelMA) hydrogels have been widely used for various biomedical applications due to their suitable biological properties and tunable physical characteristics. Three dimensional (3D) GelMA hydrogels closely resemble some essential properties of native extracellular matrix (ECM) due to the presence of cell-attaching and matrix metalloproteinase responsive peptide motifs, which allow cells to proliferate and spread in GelMA-based scaffolds. GelMA is also versatile from a processing perspective. It crosslinks when exposed to light irradiation to form hydrogels with tunable mechanical properties which mimic the native ECM. It can also be microfabricated using different methodologies including micromolding, photomasking, bioprinting, self-assembly, and microfluidic techniques to generate constructs with controlled architectures. Hybrid hydrogel systems can also be formed by mixing GelMA with nanoparticles such as carbon nanotubes and graphene oxide, and other polymers to form networks with desired combined properties and characteristics for specific biological applications. Recent research has demonstrated the proficiency of GelMA-based hydrogels in a wide range of applications including engineering of bone, cartilage, cardiac, and vascular tissues, among others. Other applications of GelMA hydrogels, besides tissue engineering, include fundamental single-single cell research, cell signaling, drug and gene delivery, and bio-sensing. PMID:26414409

Heavy metal removal by caustic-treated yeast immobilized in alginate

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

Lu, Y.; Wilkins, E.

1995-12-31

Saccharomyces cerevisiae yeast biomass was treated with hot alkali to increase its biosorption capacity for heavy metals and then was immobilized in alginate gel. Biosorption capacities for Cu{sup 2+}, Cd{sup 2+}, and Zn{sup 2+} on alginate gel, native yeast, native yeast immobilized in alginate gel, and caustic-treated yeast immobilized in alginate gel were all compared. Immobilized yeasts could be reactivated and reused in a manner similar to the ion exchange resins. Immobilized caustic-treated yeast has high heavy metal biosorption capacity and high metal removal efficiency in a rather wide acidic pH region. The biosorption isotherm of immobilized caustic-treated yeast wasmore » studied, and empirical equations were obtained. The initial pH of polluted water affected the metal removal efficiency significantly, and the equilibrium biosorption capacity seemed to be temperature independent at lower initial metal concentrations.« less

Modeling of glucose release from native and modified wheat starch gels during in vitro gastrointestinal digestion using artificial intelligence methods.

PubMed

Yousefi, A R; Razavi, Seyed M A

2017-04-01

Estimation of the amounts of glucose release (AGR) during gastrointestinal digestion can be useful to identify food of potential use in the diet of individuals with diabetes. In this work, adaptive neuro-fuzzy inference system (ANFIS), genetic algorithm-artificial neural network (GA-ANN) and group method of data handling (GMDH) models were applied to estimate the AGR from native (NWS), cross-linked (CLWS) and hydroxypropylated wheat starch (HPWS) gels during digestion under simulated gastrointestinal conditions. The GA-ANN and ANFIS were fed with 3 inputs of digestion time (1-120min), gel volume (7.5 and 15ml) and concentration (8 and 12%, w/w) for prediction of the AGR. The developed ANFIS predictions were close to the experimental data (r=0.977-0.996 and RMSE=0.225-0.619). The optimized GA-ANN, which included 6-7 hidden neurons, predicted the AGR with a good precision (r=0.984-0.993 and RMSE=0.338-0.588). Also, a three layers GMDH model with 3 neurons accurately predicted the AGR (r=0.979-0.986 and RMSE=0.339-0.443). Sensitivity analysis data demonstrated that the gel concentration was the most sensitive factor for prediction of the AGR. The results dedicated that the AGR will be accurately predictable through such soft computing methods providing less computational cost and time. Copyright © 2017 Elsevier B.V. All rights reserved.

A novel collagen hydrogel cross-linked by gamma-ray irradiation in acidic pH conditions.

PubMed

Inoue, Naoki; Bessho, Masahiko; Furuta, Masakazu; Kojima, Takao; Okuda, Shuichi; Hara, Masayuki

2006-01-01

We made a new type of collagen gel by gamma-ray irradiation of an acidic solution of type-I collagen, and performed comparative studies on a conventional gel and the new type of gel. The neutral gel, a conventional 0.3% (w/v) collagen gel, was formed at neutral pH and then irradiated by gamma-rays. The acidic gel, a 0.3% (w/v) collagen gel, was formed directly from the acidic solution of collagen by y-ray irradiation. Both types of gel were prepared, swollen in water and then dried for the measurement of specific water content. The neutral gel showed a relatively high specific water content and shrunk moderately, depending on the dose, while the acidic gel showed lower specific water content and shrunk clearly by y-ray irradiation. A three-dimensional tangled network of microfibrils was clearly observed in the neutral gels by scanning electron microscopy, but not in the acidic gels. From these results, we concluded that the acidic gel was quite different from a conventional collagen gel. Sodium dodecylsulfate-polyacrylamide gel electrophoresis showed that the alpha1 subunit and alpha2 subunit of the collagen molecule were cross-linked. The triple-helical structure of collagen was only partially perturbed, but not denatured completely, because the circular dichroism spectrum of the collagen solution irradiated at 1.3 kGy was similar to that of native collagen solution. Amino-acid analysis revealed that tyrosine, phenylalanine and histidine decreased by irradiation in the neutral gel. In the case of the acidic gel, these three amino acids and methionine decreased. We considered that these amino acids were cross-linking points between the collagen subunits during the gamma-ray irradiation.

Effect of heat-moisture treatment on the structural, physicochemical, and rheological characteristics of arrowroot starch.

PubMed

Pepe, Larissa S; Moraes, Jaqueline; Albano, Kivia M; Telis, Vânia R N; Franco, Célia M L

2016-04-01

The effect of heat-moisture treatment on structural, physicochemical, and rheological characteristics of arrowroot starch was investigated. Heat-moisture treatment was performed with starch samples conditioned to 28% moisture at 100 ℃ for 2, 4, 8, and 16 h. Structural and physicochemical characterization of native and modified starches, as well as rheological assays with gels of native and 4 h modified starches subjected to acid and sterilization stresses were performed. Arrowroot starch had 23.1% of amylose and a CA-type crystalline pattern that changed over the treatment time to A-type. Modified starches had higher pasting temperature and lower peak viscosity while breakdown viscosity practically disappeared, independently of the treatment time. Gelatinization temperature and crystallinity increased, while enthalpy, swelling power, and solubility decreased with the treatment. Gels from modified starches, independently of the stress conditions, were found to have more stable apparent viscosities and higher G' and G″ than gels from native starch. Heat-moisture treatment caused a reorganization of starch chains that increased molecular interactions. This increase resulted in higher paste stability and strengthened gels that showed higher resistance to shearing and heat, even after acid or sterilization conditions. A treatment time of 4 h was enough to deeply changing the physicochemical properties of starch. © The Author(s) 2015.

Direct analysis of in-gel proteins by carbon nanotubes-modified paper spray ambient mass spectrometry.

PubMed

Han, Feifei; Yang, Yuhan; Ouyang, Jin; Na, Na

2015-02-07

The in situ and direct extraction, desorption and ionization of in-gel intact proteins after electrophoresis has been achieved by carbon nanotubes (CNTs)-modified paper spray mass spectrometry at ambient conditions. Characteristics of CNTs (including larger surface area, smaller pore diameter and enhanced conductivity) were endowed to the porous filter paper substrate by uniformly dispersing the CNTs on the filter paper. Upon applying electric potential to the CNTs-modified paper, the in-gel proteins were extracted from the gel and subsequently migrated to the tip of the filter paper by electrophoresis-like behavior for paper spray ionization, which was monitored by extracted ion chronograms. The characterizations of modified filter papers and CNTs nanoparticles further confirmed the role of CNTs in in-gel protein extraction, protein migration as well as spray ionization at the paper tip. Under optimized conditions, a mixture of cytochrome c, lysozyme and myoglobin was successfully separated by native electrophoresis and subsequently analysed by the present method, showing a limit of detection of 10 ng per gel band. The present strategy offers a new pathway for the direct detection of in-gel intact proteins at ambient conditions without any pre-treatment (e.g. digestion, chemical extraction and desalting), which exhibits potential applications in top-down proteomics.

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

PubMed

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

2014-03-01

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

Suppression of Listeria monocytogenes by the Native Micro-Flora in Teewurst Sausage.

PubMed

Austin-Watson, Clytrice; Grant, Ar'Quette; Brice, Michline

2013-10-21

Modern consumers are interested in the use of non-chemical methods to control pathogens when heat sterilization is not an option. Such is the case with teewurst sausage, a raw spreadable sausage and a popular German commodity. Although Listeria was not found in teewurst, the optimal microbial growing conditions of teewurst coupled with the ubiquity of L. monocytogenes in nature, makes the possibility of contamination of products very possible. This pilot study was conducted to examine teewurst's native micro-flora's ability to suppress the outgrowth of L. monocytogenes at 10 °C using standard plate counts and PCR-DGGE. Traditional plating methods showed L. monocytogenes growth significantly decreased when in competition with the teewurst's native micro-flora ( p < 0.05). The native micro-flora of the teewurst suppressed the overall growth of L. monocytogenes by an average of two logs, under these conditions. Denaturing Gradient Gel Electrophoresis (DGGE) amplicons with unique banding patterns were extracted from DGGE gel for identification. Brochothrix thermosphacta and Lactobacillus curvatus were identified as a part of the teewurst's native micro-flora. Although the native micro-flora did not decrease L. monocytogenes to below limits of detection, it was enough of a decrease to warrant further investigation.

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

PubMed

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

2017-06-21

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

Purification and characterization of a soluble glycoprotein from garlic (Allium sativum) and its in vitro bioactivity.

PubMed

Wang, Yan; Zou, Tingting; Xiang, Minghui; Jin, Chenzhong; Zhang, Xuejiao; Chen, Yong; Jiang, Qiuqing; Hu, Yihong

2016-10-02

A soluble glycoprotein was purified to homogeneity from ripe garlic (Allium sativum) bulbs using ammonium sulfate precipitation, Sephadex G-100 gel filtration, and diethylaminoethyl-52 cellulose anion-exchange chromatography. A native mass of 55.7 kDa estimated on gel permeation chromatography and a molecular weight of 13.2 kDa observed on sodium dodecyl sulfate-polyacrylamide gel electrophoresis supported that the glycoprotein is a homotetramer. β-Elimination reaction result suggested that the glycoprotein is an N-linked type. Fourier-transform infrared spectroscopy proved that it contains sugar. Gas chromatography-mass spectrometer analysis showed that its sugar component was galactose. The glycoprotein has 1,1-diphenyl-2-picrylhydrazil free radical scavenging activity and the peroxidation inhibition ability to polyunsaturated fatty acid. These results indicated that the glycoprotein has potential for food additives, functional foods, and even biotechnological and medical applications.

Evaluation of Electrospun Nanofiber-Anchored Silicone for the Degenerative Intervertebral Disc

PubMed Central

Riahanizad, S.

2017-01-01

The nucleus pulposus (NP) substitution by polymeric gel is one of the promising techniques for the repair of the degenerative intervertebral disc (IVD). Silicone gel is one of the potential candidates for a NP replacement material. Electrospun fiber anchorage to silicone disc, referred as ENAS disc, may not only improve the biomechanical performances of the gel but it can also improve restoration capability of the gel, which is unknown. This study successfully produced a novel process to anchor any size and shape of NP gel with electrospun fiber mesh. Viscoelastic properties of silicone and ENAS disc were measured using standard experimental techniques and compared with the native tissue properties. Ex vivo mechanical tests were conducted on ENAS disc-implanted rabbit tails to the compare the mechanical stability between intact and ENAS implanted spines. This study found that viscoelastic properties of ENAS disc are higher than silicone disc and comparable to the viscoelastic properties of human NP. The ex vivo studies found that the ENAS disc restore the mechanical functionality of rabbit tail spine, after discectomy of native NP and replacing the NP by ENAS disc. Therefore, the PCL ENF mesh anchoring technique to a NP implant can have clinical potential. PMID:29181144

Purification and characterization of tannase from Paecilomyces variotii: hydrolysis of tannic acid using immobilized tannase.

PubMed

Mahendran, B; Raman, N; Kim, D-J

2006-04-01

An extracellular tannase (tannin acyl hydrolase) was isolated from Paecilomyces variotii and purified from cell-free culture filtrate using ammonium sulfate precipitation followed by ion exchange and gel filtration chromatography. Fractional precipitation of the culture filtrate with ammonium sulfate yielded 78.7% with 13.6-folds purification, and diethylaminoethyl-cellulose column chromatography and gel filtration showed 19.4-folds and 30.5-folds purifications, respectively. Molecular mass of tannase was found 149.8 kDa through native polyacrylamide gel electrophoresis (PAGE) analysis. Sodium dodecyl sulphate-PAGE revealed that the purified tannase was a monomeric enzyme with a molecular mass of 45 kDa. Temperature of 30 to 50 degrees C and pH of 5.0 to 7.0 were optimum for tannase activity and stability. Tannase immobilized on alginate beads could hydrolyze tannic acid even after extensive reuse and retained about 85% of the initial activity. Thin layer chromatography, high performance liquid chromatography, and (1)H-nuclear magnetic resonance spectral analysis confirmed that gallic acid was formed as a byproduct during hydrolysis of tannic acid.

Suppression of Listeria monocytogenes by the Native Micro-Flora in Teewurst Sausage

PubMed Central

Austin-Watson, Clytrice; Grant, Ar’Quette; Brice, Michline

2013-01-01

Modern consumers are interested in the use of non-chemical methods to control pathogens when heat sterilization is not an option. Such is the case with teewurst sausage, a raw spreadable sausage and a popular German commodity. Although Listeria was not found in teewurst, the optimal microbial growing conditions of teewurst coupled with the ubiquity of L. monocytogenes in nature, makes the possibility of contamination of products very possible. This pilot study was conducted to examine teewurst’s native micro-flora’s ability to suppress the outgrowth of L. monocytogenes at 10 °C using standard plate counts and PCR-DGGE. Traditional plating methods showed L. monocytogenes growth significantly decreased when in competition with the teewurst’s native micro-flora (p < 0.05). The native micro-flora of the teewurst suppressed the overall growth of L. monocytogenes by an average of two logs, under these conditions. Denaturing Gradient Gel Electrophoresis (DGGE) amplicons with unique banding patterns were extracted from DGGE gel for identification. Brochothrix thermosphacta and Lactobacillus curvatus were identified as a part of the teewurst’s native micro-flora. Although the native micro-flora did not decrease L. monocytogenes to below limits of detection, it was enough of a decrease to warrant further investigation. PMID:28239131

Native PAGE to study the interaction between the oncosuppressor p53 and its protein ligands.

PubMed

Lamberti, Anna; Sgammato, Roberta; Desiderio, Doriana; Punzo, Chiara; Raimo, Gennaro; Novellino, Ettore; Carotenuto, Alfonso; Masullo, Mariorosario

2015-02-01

In the present study, we investigated a new approach for studying the interaction between p53 and MDM2/X (where MDM is murine double minute protein). The method is based on the different mobility between the interacting domains of the oncosuppressor p53 and its protein ligands MDM2/X on polyacrylamide gels under native conditions. While the two proteins MDM2/X alone were able to enter the gel, the formation of a binary complex between p53 and MDM2/X prevented the gel entry. The novel technique is reliable for determining the different affinity elicited by MDM2 or MDMX toward p53, and can be useful for analyzing the dissociation power exerted by other molecules on the p53-MDM2/X complex. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A brief review of other notable protein blotting methods.

PubMed

Kurien, Biji T; Scofield, R Hal

2009-01-01

A plethora of methods have been used for transferring proteins from the gel to the membrane. These include centrifuge blotting, electroblotting of proteins to Teflon tape and membranes for N- and C-terminal sequence analysis, multiple tissue blotting, a two-step transfer of low and high molecular weight proteins, blotting of Coomassie Brilliant Blue (CBB)-stained proteins from polyacrylamide gels to transparencies, acid electroblotting onto activated glass, membrane-array method for the detection of human intestinal bacteria in fecal samples, protein microarray using a new black cellulose nitrate support, electrotransfer using square wave alternating voltage for enhanced protein recovery, polyethylene glycol-mediated significant enhancement of the immunoblotting transfer, parallel protein chemical processing before and during western blot and the molecular scanner concept, electronic western blot of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-identified polypeptides from parallel processed gel-separated proteins, semidry electroblotting of peptides and proteins from acid-urea polyacrylamide gels, transfer of silver-stained proteins from polyacrylamide gels to polyvinylidene difluoride (PVDF) membranes, and the display of K(+) channel proteins on a solid nitrocellulose support for assaying toxin binding. The quantification of proteins bound to PVDF membranes by elution of CBB, clarification of immunoblots on PVDF for transmission densitometry, gold coating of nonconductive membranes before MALDI tandem mass spectrometric analysis to prevent charging effect for analysis of peptides from PVDF membranes, and a simple method for coating native polysaccharides onto nitrocellulose are some of the methods involving either the manipulation of membranes with transferred proteins or just a passive transfer of antigens to membranes. All these methods are briefly reviewed in this chapter.

The effects of scaffold architecture and fibrin gel addition on tendon cell phenotype.

PubMed

Pawelec, K M; Wardale, R J; Best, S M; Cameron, R E

2015-01-01

Development of tissue engineering scaffolds relies on careful selection of pore architecture and chemistry of the cellular environment. Repair of skeletal soft tissue, such as tendon, is particularly challenging, since these tissues have a relatively poor healing response. When removed from their native environment, tendon cells (tenocytes) lose their characteristic morphology and the expression of phenotypic markers. To stimulate tendon cells to recreate a healthy extracellular matrix, both architectural cues and fibrin gels have been used in the past, however, their relative effects have not been studied systematically. Within this study, a combination of collagen scaffold architecture, axial and isotropic, and fibrin gel addition was assessed, using ovine tendon-derived cells to determine the optimal strategy for controlling the proliferation and protein expression. Scaffold architecture and fibrin gel addition influenced tendon cell behavior independently in vitro. Addition of fibrin gel within a scaffold doubled cell number and increased matrix production for all architectures studied. However, scaffold architecture dictated the type of matrix produced by cells, regardless of fibrin addition. Axial scaffolds, mimicking native tendon, promoted a mature matrix, with increased tenomodulin, a marker for mature tendon cells, and decreased scleraxis, an early transcription factor for connective tissue. This study demonstrated that both architectural cues and fibrin gel addition alter cell behavior and that the combination of these signals could improve clinical performance of current tissue engineering constructs.

Histidinoalanine, a naturally occurring cross-link derived from phosphoserine and histidine residues in mineral-binding phosphoproteins.

PubMed

Marsh, M E

1986-05-06

Native mineral-containing phosphoprotein particles were isolated from the Heterodont bivalve Macrocallista nimbosa. The native particles are discrete structures about 40 nm in diameter which migrate as a single band during electrophoresis in agarose gels. Removal of the mineral component with ethylenediaminetetraacetic acid dissociates the native protein into nonidentical subunits. The lower molecular weight subunits, representing 8% of the total protein, were obtained by differential centrifugation. The native protein is characterized by a high content of aspartic acid, phosphoserine, phosphothreonine, histidine, and the bifunctional cross-linking residue histidinoalanine. The low molecular weight subunits have the same amino acid composition except for a reduction in histidinoalanine and a corresponding increase in phosphoserine and histidine residues, demonstrating that the alanine portion of the cross-link is derived from phosphoserine residues. Ion-exchange chromatography and molecular sieve chromatography show that the low molecular weight subunits have a similar charge density but differ in molecular weight, and the relative mobilities of the subunits on agarose gels indicate that they are polymers of a single phosphoprotein molecule. The minimum molecular weight of the monomer is about 140 000 on the basis of the amino acid composition. The high molecular weight subunits are rich in histidinoalanine and too large to be resolved by either molecular sieve chromatography or gel electrophoresis. On the basis of the ultrastructural, electrophoretic, chromatographic, and compositional evidence, native phosphoprotein particles are composed of subunits ionically cross-linked via divalent cations. These subunits are variable molecular weight aggregates of a single phosphoprotein molecule covalently cross-linked via histidinoalanine residues. Evidence for a nonenzymatic cross-linking mechanism is discussed.

The box C/D sRNP dimeric architecture is conserved across domain Archaea

PubMed Central

Bower-Phipps, Kathleen R.; Taylor, David W.; Wang, Hong-Wei; Baserga, Susan J.

2012-01-01

Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2′-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species—Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus—indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain. PMID:22753779

The box C/D sRNP dimeric architecture is conserved across domain Archaea.

PubMed

Bower-Phipps, Kathleen R; Taylor, David W; Wang, Hong-Wei; Baserga, Susan J

2012-08-01

Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2'-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species--Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus--indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.

The structure of high-methoxyl sugar acid gels of citrus pectin as determined by AFM

USDA-ARS?s Scientific Manuscript database

Images of native high methoxyl sugar acid gels (HMSAG) were obtained by atomic force microscopy (AFM) in the Tapping ModeTM. Electronic thinning of the pectin strands to one pixel wide allowed the pectin network to be viewed in the absence of variable strand widths related to preferentially solvate...

Digital-Micromirror-Device Projection Printing System for Meniscus Tissue Engineering

PubMed Central

Grogan, Shawn P; Chung, Peter H; Soman, Pranav; Chen, Peter; Lotz, Martin K; Chen, Shaochen; D’Lima, Darryl D

2013-01-01

Meniscus degeneration due to age or injury can lead to osteoarthritis. Though promising, current cell-based approaches show limited success. Here we present three-dimensional methacrylated gelatin (GelMA) scaffolds patterned via projection stereolithography to emulate the circumferential alignment of cells in native meniscus tissue. Cultured human avascular zone meniscus cells from normal meniscus were seeded on the scaffolds. Cell viability was monitored, and neo-tissue formation was assessed by gene expression analysis and histology after two weeks in serum free culture with TGFβ1 (10ng/ml). Light, confocal and scanning electron microscopy was used to observe cell/GelMA interactions. Tensile mechanical testing was performed on unseeded, fresh scaffolds and two-week old cell-seeded and unseeded scaffolds. Two-week old cell/GelMA constructs were implanted into surgically created meniscus defects in an explant organ culture model. No cytotoxic effects were observed three weeks after implantation, and cells grew and aligned to the patterned GelMA strands. Gene expression profiles and histology indicated promotion of a fibrocartilage-like meniscus phenotype, and scaffold integration with repair tissue was observed in the explant model. We show that micropatterned GelMA scaffolds are non-toxic, produce organized cellular alignment, and promote meniscus-like tissue formation. Prefabrication of GelMA scaffolds with architectures mimicking meniscus collagen bundle organization shows promise for meniscal repair. Furthermore, the technique presented may be scaled to repair larger defects. PMID:23523536

Dimethylformamide interferes with Coomassie dye staining of proteins on blue native gel electrophoresis.

PubMed

Raghupathy, V; Oommen, Anna; Ramachandran, Anup

2014-06-15

Blue native gel electrophoresis (BN-PAGE) is used extensively for characterization of mitochondrial respiratory complexes and uses the binding of Coomassie brilliant blue G-250 to visualize proteins. Oxidative modification of sulfhydryl groups of such proteins can be evaluated by labeling with iodoacetamide conjugated to biotin (BIAM) and detected with streptavidin peroxidase on Western blots following BN-PAGE. However, dissolving BIAM in dimethylformamide, a recommended solvent, reduces Coomassie blue G staining to proteins during BN-PAGE. This interference is prevented by dissolving BIAM in dimethyl sulfoxide. Precautions in the use of the dye for protein staining subsequent to BIAM labeling are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Selective staining of proteins with hydrophobic surface sites on a native electrophoretic gel.

PubMed

Bertsch, Martina; Kassner, Richard J

2003-01-01

Chemical proteomics aims to characterize all of the proteins in the proteome with respect to their function, which is associated with their interaction with other molecules. We propose the identification of a subproteomic library of expressed proteins whose native structures are typified by the presence of hydrophobic surface sites, which are often involved in interactions with small molecules, membrane lipids, and other proteins, pertaining to their functions. We demonstrate that soluble globular proteins with hydrophobic surface sites can be detected selectively by staining on an electrophoretic gel run under nondenaturing conditions. The application of these staining techniques may help elucidate new catalytic, transport, and regulatory functionalities in complex proteomic screenings.

Datasets depicting mobility retardation of NCS proteins observed upon incubation with calcium, but not with magnesium, barium or strontium.

PubMed

Viviano, Jeffrey; Krishnan, Anuradha; Scully, Jenna; Wu, Hao; Venkataraman, Venkat

2016-06-01

In this data article we show the specificity of the Ca(2+)-induced mobility shift in three proteins that belong to the neuronal calcium sensor (NCS) protein family: Hippocalcin, GCAP1 and GCAP2. These proteins did not display a shift in mobility in native gels when incubated with divalent cations other than Ca(2+) - such as Mg(2+), Ba(2+), and Sr(2+), even at 10× concentrations. The data is similar to that obtained with another NCS protein, neurocalcin delta (Viviano et al., 2016, "Electrophoretic Mobility Shift in Native Gels Indicates Calcium-dependent Structural Changes of Neuronal Calcium Sensor Proteins", [1]).

Influence of pH on viscoelastic properties of heat-induced gels obtained with a β-Lactoglobulin fraction isolated from bovine milk whey hydrolysates.

PubMed

Estévez, Natalia; Fuciños, Pablo; Bargiela, Verónica; Picó, Guillermo; Valetti, Nadia Woitovich; Tovar, Clara Asunción; Rúa, M Luisa

2017-03-15

A β-Lactoglobulin fraction (r-βLg) was isolated from whey hydrolysates produced with cardosins from Cynara cardunculus. The impact of the hydrolysis process on the r-βLg structure and the rheological properties of heat-induced gels obtained thereafter were studied at different pH values. Differences were observed between r-βLg and commercial β-Lg used as control. Higher values for the fluorescence emission intensity and red shifts of the emission wavelength of r-βLg suggested changes in its tertiary structure and more solvent-exposed tryptophan residues. Circular dichroism spectra also supported these evidences indicating that hydrolysis yielded an intermediate (non-native) β-Lg state. The thermal history of r-βLg through the new adopted conformation improved the microstructure of the gels at acidic pH. So, a new microstructure with better rheological characteristics (higher conformational flexibility and lower rigidity) and greater water holding ability was founded for r-βLg gel. These results were reflected in the microstructural analysis by scanning electron microscopy. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Sol-Gel-Modified Poly(methyl methacrylate) Electrophoresis Microchip with a Hydrophilic Channel Wall

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

Chen, Gang; Xu, Xuejiao; Lin, Yuehe

2007-07-27

A sol-gel method was employed to fabricate a poly(methyl methacrylate) (PMMA) electrophoresis microchip that contains a hydrophilic channel wall. To fabricate such a device, tetraethoxysilane (TEOS) was injected into the PMMA channel and was allowed to diffuse into the surface layer for 24 h. After removing the excess TEOS, the channel was filled with an acidic solution for 3 h. Subsequently, the channel was flushed with water and was pretreated in an oven to obtain a sol-gel-modified PMMA microchip. The water contact angle for the sol-gel-modified PMMA was 27.4° compared with 66.3° for the pure PMMA. In addition, the electro-osmoticmore » flow increased from 2.13×10-4 cm2 V-1 s-1 for the native-PMMA channel to 4.86×10-4 cm2 V-1 s-1 for the modified one. The analytical performance of the sol-gel-modified PMMA microchip was demonstrated for the electrophoretic separation of several purines, coupled with amperometric detection. The separation efficiency of uric acid increased to 74 882.3 m-1 compared with 14 730.5 m-1 for native-PMMA microchips. The result of this simple modification is a significant improvement in the performance of PMMA for microchip electrophoresis and microfluidic applications.« less

Impaired Lysosomal Trimming of N-Linked Oligosaccharides Leads to Hyperglycosylation of Native Lysosomal Proteins in Mice with α-Mannosidosis ▿

PubMed Central

Damme, Markus; Morelle, Willy; Schmidt, Bernhard; Andersson, Claes; Fogh, Jens; Michalski, Jean-Claude; Lübke, Torben

2010-01-01

α-Mannosidosis is caused by the genetic defect of the lysosomal α-d-mannosidase (LAMAN), which is involved in the breakdown of free α-linked mannose-containing oligosaccharides originating from glycoproteins with N-linked glycans, and thus manifests itself in an extensive storage of mannose-containing oligosaccharides. Here we demonstrate in a model of mice with α-mannosidosis that native lysosomal proteins exhibit elongated N-linked oligosaccharides as shown by two-dimensional difference gel electrophoresis, deglycosylation assays, and mass spectrometry. The analysis of cathepsin B-derived oligosaccharides revealed a hypermannosylation of glycoproteins in mice with α-mannosidosis as indicated by the predominance of extended Man3GlcNAc2 oligosaccharides. Treatment with recombinant human α-mannosidase partially corrected the hyperglycosylation of lysosomal proteins in vivo and in vitro. These data clearly demonstrate that LAMAN is involved not only in the lysosomal catabolism of free oligosaccharides but also in the trimming of asparagine-linked oligosaccharides on native lysosomal proteins. PMID:19884343

Monitoring refolding of tailspike endorhamnosidase using capillary electrophoresis-laser induced tryptophan fluorescence

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

Jensen, P.K.; Lee, Cheng S.; King, J.A.

1997-12-31

The use of capillary electrophoresis equipped with laser-induced tryptophan fluorescence detection is presented for monitoring the refolding pathway of phage P22 tailspike endorhamnosidase. Upon initiation of refolding, tailspike polypeptides rapidly fold into structured monomeric intermediates with a high content of secondary structure. These monomeric species associate to form the triple-chain defined folding intermediates, the protrimers. Conversion of the protrimer into the native, sodium dodecyl sulfate (SDS) resistant tailspike protein is the rate-limiting step in the refolding pathway. Refolding kinetics and yield measured by capillary electrophoresis are in good agreement with those obtained via native gel electrophoresis, SDS polyacrylamide gel electrophoresismore » (SDS-PAGE) and fluorescence spectrophotometry. To enhance separation resolution between protrimer and native protein in capillary electrophoresis, the use of poly(ethylene oxide) is investigated for the introduction of a sieving separation mechanism. The increased viscosity of the electrophoresis buffer may also play a role in resolution enhancement.« less

Modification of solubility and heat-induced gelation of amaranth 11S globulin by protein engineering.

PubMed

Carrazco-Peña, Laura; Osuna-Castro, Juan A; De León-Rodríguez, Antonio; Maruyama, Nobuyuki; Toro-Vazquez, Jorge F; Morales-Rueda, Juan A; Barba de la Rosa, Ana P

2013-04-10

The primary structure of amaranth 11S globulin (Ah11S) was engineered with the aim to improve its functional properties. Four continuous methionines were inserted in variable region V, obtaining the Ah11Sr+4M construction. Changes on protein structure and surface characteristics were analyzed in silico. Solubility and heat-induced gelation of recombinant amaranth 11S proglobulin (Ah11Sr and Ah11Sr+4M) were compared with the native protein (Ah11Sn) purified from amaranth seed flour. The Ah11Sr+4 M showed the highest surface hydrophobicity, but as consequence the solubility was reduced. At low ionic strength (μ = 0.2) and acidic pH (<4.1), the recombinant proteins Ah11Sr and Ah11Sr+4 M had the highest and lowest solubility values, respectively. All globulins samples formed gels at 90 °C and low ionic strength, but Ah11Sn produced the weakest and Ah11Sr the strongest gels. Differential scanning calorimetry analysis under gel forming conditions revealed only exothermic transitions for all amaranth 11S globulins analyzed. In conclusion, the 3D structure analysis has revealed interesting molecular features that could explain the thermal resistance and gel forming ability of amaranth 11S globulins. The incorporation of four continuous methionines in amaranth increased the hydrophobicity, and self-supporting gels formed had intermediate hardness between Ah11Sn and Ah11Sr. These functional properties could be used in the food industry for the development of new products based on amaranth proteins.

[Tissue-specific nucleoprotein complexes].

PubMed

Riadnova, I Iu; Shataeva, L K; Khavinson, V Kh

2000-01-01

A method of isolation of native nucleorprotein complexes from cattle cerebral cortex, thymus, and liver was developed. Compositions of these complexes were studied by means of gel-chromatography and ion-exchange chromatography. These preparations were shown to consist of several fractions of proteins and their complexes differ by molecular mass and electro-chemical properties. Native nucleoprotein complexes revealed high tissue specific activity, which was not species-specific.

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

Wang, Xiaochun; Wei, Yihao; Shi, Lanxin

Glutamine synthetase (GS; EC 6.3.1.2) plays a crucial role in the assimilation and re-assimilation of ammonia derived from a wide variety of metabolic processes during plant growth and development. Here, three developmentally regulated isoforms of GS holoenzyme in the leaf of wheat ( Triticum aestivum L.) seedlings are described using native-PAGE with a transferase activity assay. The isoforms showed different mobilities in gels, with GSII>GSIII>GSI. The cytosolic GSI was composed of three subunits, GS1, GSr1, and GSr2, with the same molecular weight (39.2kDa), but different pI values. GSI appeared at leaf emergence and was active throughout the leaf lifespan. GSIImore » and GSIII, both located in the chloroplast, were each composed of a single 42.1kDa subunit with different pI values. GSII was active mainly in green leaves, while GSIII showed brief but higher activity in green leaves grown under field conditions. LC-MS/MS experiments revealed that GSII and GSIII have the same amino acid sequence, but GSII has more modification sites. With a modified blue native electrophoresis (BNE) technique and in-gel catalytic activity analysis, only two GS isoforms were observed: one cytosolic and one chloroplastic. Mass calibrations on BNE gels showed that the cytosolic GS1 holoenzyme was ~490kDa and likely a dodecamer, and the chloroplastic GS2 holoenzyme was ~240kDa and likely a hexamer. Lastly, our experimental data suggest that the activity of GS isoforms in wheat is regulated by subcellular localization, assembly, and modification to achieve their roles during plant development.« less

Digital micromirror device projection printing system for meniscus tissue engineering.

PubMed

Grogan, Shawn P; Chung, Peter H; Soman, Pranav; Chen, Peter; Lotz, Martin K; Chen, Shaochen; D'Lima, Darryl D

2013-07-01

Meniscus degeneration due to age or injury can lead to osteoarthritis. Although promising, current cell-based approaches show limited success. Here we present three-dimensional methacrylated gelatin (GelMA) scaffolds patterned via projection stereolithography to emulate the circumferential alignment of cells in native meniscus tissue. Cultured human avascular zone meniscus cells from normal meniscus were seeded on the scaffolds. Cell viability was monitored, and new tissue formation was assessed by gene expression analysis and histology after 2weeks in serum-free culture with transforming growth factor β1 (10ngml(-1)). Light, confocal and scanning electron microscopy were used to observe cell-GelMA interactions. Tensile mechanical testing was performed on unseeded, fresh scaffolds and 2-week-old cell-seeded and unseeded scaffolds. 2-week-old cell-GelMA constructs were implanted into surgically created meniscus defects in an explant organ culture model. No cytotoxic effects were observed 3weeks after implantation, and cells grew and aligned to the patterned GelMA strands. Gene expression profiles and histology indicated promotion of a fibrocartilage-like meniscus phenotype, and scaffold integration with repair tissue was observed in the explant model. We show that micropatterned GelMA scaffolds are non-toxic, produce organized cellular alignment, and promote meniscus-like tissue formation. Prefabrication of GelMA scaffolds with architectures mimicking the meniscus collagen bundle organization shows promise for meniscal repair. Furthermore, the technique presented may be scaled up to repair larger defects. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Other notable protein blotting methods: a brief review.

PubMed

Kurien, Biji T; Scofield, R Hal

2015-01-01

Proteins have been transferred from the gel to the membrane by a variety of methods. These include vacuum blotting, centrifuge blotting, electroblotting of proteins to Teflon tape and membranes for N- and C-terminal sequence analysis, multiple tissue blotting, a two-step transfer of low- and high-molecular-weight proteins, acid electroblotting onto activated glass, membrane-array method for the detection of human intestinal bacteria in fecal samples, protein microarray using a new black cellulose nitrate support, electrotransfer using square wave alternating voltage for enhanced protein recovery, polyethylene glycol-mediated significant enhancement of the immunoblotting transfer, parallel protein chemical processing before and during western blot and the molecular scanner concept, electronic western blot of matrix-assisted laser desorption/ionization mass spectrometric-identified polypeptides from parallel processed gel-separated proteins, semidry electroblotting of peptides and proteins from acid-urea polyacrylamide gels, transfer of silver-stained proteins from polyacrylamide gels to polyvinylidene difluoride (PVDF) membranes, and the display of K(+) channel proteins on a solid nitrocellulose support for assaying toxin binding. The quantification of proteins bound to PVDF membranes by elution of CBB, clarification of immunoblots on PVDF for transmission densitometry, gold coating of nonconductive membranes before matrix-assisted laser desorption/ionization tandem mass spectrometric analysis to prevent charging effect for analysis of peptides from PVDF membranes, and a simple method for coating native polysaccharides onto nitrocellulose are some of the methods involving either the manipulation of membranes with transferred proteins or just a passive transfer of antigens to membranes. All these methods are briefly reviewed in this chapter.

Effects of Size and Stability of Native Fat Globules on the Formation of Milk Gel Induced by Rennet.

PubMed

Luo, Jie; Wang, Yuhan; Guo, Huiyuan; Ren, Fazheng

2017-03-01

Rennet-induced gelation crucially impacts cheese structure. In this study, effects of the size and stability of native fat globules on the kinetics of rennet-induced coagulation were revealed by determining the caseinomacropeptide release rate and rheological properties of milk. Moreover, the mobility and stability of fat globules during renneting was revealed using diffusing wave spectroscopy and confocal laser scanning microscopy. By use of a 2-stage gravity separation combined centrifugation scheme, native fat globules were selectively separated into small (SFG, D 4,3 = 1.87 ± 0.02 μm) and large fat globules (LFG, D 4,3 = 5.65 ± 0.03 μm). The protein and fat content of SFG and LFG milk were then standardized to 3.2 g/100 mL and 1.2 g/100 mL, respectively. The milk containing different sized globules were then subjected to renneting experiments in the laboratory. Reduction of globule size accelerated the aggregation of casein micelles during renneting, giving a shorter gelation time and earlier 1/l * change. The gel produced from LFG milk was broken due to coalescent fat globules and generated coarser gel strands compared to the finer strands formed with SFG milk. Structural differences were also confirmed with a higher final storage modulus of the curd made from SFG milk than that from the LFG. In conclusion, the size of fat globules affects the aggregation of casein micelles. Moreover, fat globule coalescence and creaming during renneting, also affects the structure of the rennet gel. A better understanding of the size of globules effect on milk gelation could lead to the development of cheese with specific properties. © 2017 Institute of Food Technologists®.

Purification and sequence analysis of 4-methyl-5-nitrocatechol oxygenase from Burkholderia sp. strain DNT.

PubMed Central

Haigler, B E; Suen, W C; Spain, J C

1996-01-01

4-Methyl-5-nitrocatechol (MNC) is an intermediate in the degradation of 2,4-dinitrotoluene by Burkholderia sp. strain DNT. In the presence of NADPH and oxygen, MNC monooxygenase catalyzes the removal of the nitro group from MNC to form 2-hydroxy-5-methylquinone. The gene (dntB) encoding MNC monooxygenase has been previously cloned and characterized. In order to examine the properties of MNC monooxygenase and to compare it with other enzymes, we sequenced the gene encoding the MNC monooxygenase and purified the enzyme from strain DNT. dntB was localized within a 2.2-kb ApaI DNA fragment. Sequence analysis of this fragment revealed an open reading frame of 1,644 bp with an N-terminal amino acid sequence identical to that of purified MNC monooxygenase from strain DNT. Comparison of the derived amino acid sequences with those of other genes showed that DntB contains the highly conserved ADP and flavin adenine dinucleotide (FAD) binding motifs characteristic of flavoprotein hydroxylases. MNC monooxygenase was purified to homogeneity from strain DNT by anion exchange and gel filtration chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single protein with a molecular weight of 60,200, which is consistent with the size determined from the gene sequence. The native molecular weight determined by gel filtration was 65,000, which indicates that the native enzyme is a monomer. It used either NADH or NADPH as electron donors, and NADPH was the preferred cofactor. The purified enzyme contained 1 mol of FAD per mol of protein, which is also consistent with the detection of an FAD binding motif in the amino acid sequence of DntB. MNC monooxygenase has a narrow substrate specificity. MNC and 4-nitrocatechol are good substrates whereas 3-methyl-4-nitrophenol, 3-methyl-4-nitrocatechol, 4-nitrophenol, 3-nitrophenol, and 4-chlorocatechol were not. These studies suggest that MNC monooxygenase is a flavoprotein that shares some properties with previously studied nitrophenol oxygenases. PMID:8830701

Enhancing Accuracy in Molecular Weight Determination of Highly Heterogeneously Glycosylated Proteins by Native Tandem Mass Spectrometry.

PubMed

Wang, Guanbo; de Jong, Rob N; van den Bremer, Ewald T J; Parren, Paul W H I; Heck, Albert J R

2017-05-02

The determination of molecular weights (MWs) of heavily glycosylated proteins is seriously hampered by the physicochemical characteristics and heterogeneity of the attached carbohydrates. Glycosylation impacts protein migration during sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC) analysis. Standard electrospray ionization (ESI)-mass spectrometry does not provide a direct solution as this approach is hindered by extensive interference of ion signals caused by closely spaced charge states of broadly distributed glycoforms. Here, we introduce a native tandem MS-based approach, enabling charge-state resolution and charge assignment of protein ions including those that escape mass analysis under standard MS conditions. Using this method, we determined the MW of two model glycoproteins, the extra-cellular domains of the highly and heterogeneously glycosylated proteins CD38 and epidermal growth factor receptor (EGFR), as well as the overall MW and binding stoichiometries of these proteins in complex with a specific antibody.

Importance of casein micelle size and milk composition for milk gelation.

PubMed

Glantz, M; Devold, T G; Vegarud, G E; Lindmark Månsson, H; Stålhammar, H; Paulsson, M

2010-04-01

The economic output of the dairy industry is to a great extent dependent on the processing of milk into other milk-based products such as cheese. The yield and quality of cheese are dependent on both the composition and technological properties of milk. The objective of this study was to evaluate the importance and effects of casein (CN) micelle size and milk composition on milk gelation characteristics in order to evaluate the possibilities for enhancing gelation properties through breeding. Milk was collected on 4 sampling occasions at the farm level in winter and summer from dairy cows with high genetic merit, classified as elite dairy cows, of the Swedish Red and Swedish Holstein breeds. Comparisons were made with milk from a Swedish Red herd, a Swedish Holstein herd, and a Swedish dairy processor. Properties of CN micelles, such as their native and rennet-induced CN micelle size and their zeta-potential, were analyzed by photon correlation spectroscopy, and rennet-induced gelation characteristics, including gel strength, gelation time, and frequency sweeps, were determined. Milk parameters of the protein, lipid, and carbohydrate profiles as well as minerals were used to obtain correlations with native CN micelle size and gelation characteristics. Milk pH and protein, CN, and lactose contents were found to affect milk gelation. Smaller native CN micelles were shown to form stronger gels when poorly coagulating milk was excluded from the correlation analysis. In addition, milk pH correlated positively, whereas Mg and K correlated negatively with native CN micellar size. The milk from the elite dairy cows was shown to have good gelation characteristics. Furthermore, genetic progress in relation to CN micelle size was found for these cows as a correlated response to selection for the Swedish breeding objective if optimizing for milk gelation characteristics. The results indicate that selection for smaller native CN micelles and lower milk pH through breeding would enhance gelation properties and may thus improve the initial step in the processing of cheese. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Data on the calcium-induced mobility shift of myristoylated and non-myristoylated forms of neurocalcin delta.

PubMed

Viviano, Jeffrey; Krishnan, Anuradha; Wu, Hao; Venkataraman, Venkat

2016-06-01

This data article presents the differences observed between the myristoylated and non-myristoylated forms of the neuronal calcium sensor protein, neurocalcin delta (NCALD). Analysis of the myristoylated and non-myristoylated versions of the protein by mass spectrometry provided difference in mass values consistent with addition of myristoyl group. In the presence of calcium, mobility retardation was observed upon electrophoresis of the protein in native gels. The retardation was dose-dependent and was exhibited by both the myristoylated and non-myristoylated forms of the protein.

Three-Dimensional-Bioprinted Dopamine-Based Matrix for Promoting Neural Regeneration.

PubMed

Zhou, Xuan; Cui, Haitao; Nowicki, Margaret; Miao, Shida; Lee, Se-Jun; Masood, Fahed; Harris, Brent T; Zhang, Lijie Grace

2018-03-14

Central nerve repair and regeneration remain challenging problems worldwide, largely because of the extremely weak inherent regenerative capacity and accompanying fibrosis of native nerves. Inadequate solutions to the unmet needs for clinical therapeutics encourage the development of novel strategies to promote nerve regeneration. Recently, 3D bioprinting techniques, as one of a set of valuable tissue engineering technologies, have shown great promise toward fabricating complex and customizable artificial tissue scaffolds. Gelatin methacrylate (GelMA) possesses excellent biocompatible and biodegradable properties because it contains many arginine-glycine-aspartic acids (RGD) and matrix metalloproteinase sequences. Dopamine (DA), as an essential neurotransmitter, has proven effective in regulating neuronal development and enhancing neurite outgrowth. In this study, GelMA-DA neural scaffolds with hierarchical structures were 3D-fabricated using our custom-designed stereolithography-based printer. DA was functionalized on GelMA to synthesize a biocompatible printable ink (GelMA-DA) for improving neural differentiation. Additionally, neural stem cells (NSCs) were employed as the primary cell source for these scaffolds because of their ability to terminally differentiate into a variety of cell types including neurons, astrocytes, and oligodendrocytes. The resultant GelMA-DA scaffolds exhibited a highly porous and interconnected 3D environment, which is favorable for supporting NSC growth. Confocal microscopy analysis of neural differentiation demonstrated that a distinct neural network was formed on the GelMA-DA scaffolds. In particular, the most significant improvements were the enhanced neuron gene expression of TUJ1 and MAP2. Overall, our results demonstrated that 3D-printed customizable GelMA-DA scaffolds have a positive role in promoting neural differentiation, which is promising for advancing nerve repair and regeneration in the future.

New isoforms and assembly of glutamine synthetase in the leaf of wheat (Triticum aestivum L.)

PubMed Central

Wang, Xiaochun; Wei, Yihao; Shi, Lanxin; Ma, Xinming; Theg, Steven M.

2015-01-01

Glutamine synthetase (GS; EC 6.3.1.2) plays a crucial role in the assimilation and re-assimilation of ammonia derived from a wide variety of metabolic processes during plant growth and development. Here, three developmentally regulated isoforms of GS holoenzyme in the leaf of wheat (Triticum aestivum L.) seedlings are described using native-PAGE with a transferase activity assay. The isoforms showed different mobilities in gels, with GSII>GSIII>GSI. The cytosolic GSI was composed of three subunits, GS1, GSr1, and GSr2, with the same molecular weight (39.2kDa), but different pI values. GSI appeared at leaf emergence and was active throughout the leaf lifespan. GSII and GSIII, both located in the chloroplast, were each composed of a single 42.1kDa subunit with different pI values. GSII was active mainly in green leaves, while GSIII showed brief but higher activity in green leaves grown under field conditions. LC-MS/MS experiments revealed that GSII and GSIII have the same amino acid sequence, but GSII has more modification sites. With a modified blue native electrophoresis (BNE) technique and in-gel catalytic activity analysis, only two GS isoforms were observed: one cytosolic and one chloroplastic. Mass calibrations on BNE gels showed that the cytosolic GS1 holoenzyme was ~490kDa and likely a dodecamer, and the chloroplastic GS2 holoenzyme was ~240kDa and likely a hexamer. Our experimental data suggest that the activity of GS isoforms in wheat is regulated by subcellular localization, assembly, and modification to achieve their roles during plant development. PMID:26307137

New isoforms and assembly of glutamine synthetase in the leaf of wheat ( Triticum aestivum L.)

DOE PAGES

Wang, Xiaochun; Wei, Yihao; Shi, Lanxin; ...

2015-08-24

Glutamine synthetase (GS; EC 6.3.1.2) plays a crucial role in the assimilation and re-assimilation of ammonia derived from a wide variety of metabolic processes during plant growth and development. Here, three developmentally regulated isoforms of GS holoenzyme in the leaf of wheat ( Triticum aestivum L.) seedlings are described using native-PAGE with a transferase activity assay. The isoforms showed different mobilities in gels, with GSII>GSIII>GSI. The cytosolic GSI was composed of three subunits, GS1, GSr1, and GSr2, with the same molecular weight (39.2kDa), but different pI values. GSI appeared at leaf emergence and was active throughout the leaf lifespan. GSIImore » and GSIII, both located in the chloroplast, were each composed of a single 42.1kDa subunit with different pI values. GSII was active mainly in green leaves, while GSIII showed brief but higher activity in green leaves grown under field conditions. LC-MS/MS experiments revealed that GSII and GSIII have the same amino acid sequence, but GSII has more modification sites. With a modified blue native electrophoresis (BNE) technique and in-gel catalytic activity analysis, only two GS isoforms were observed: one cytosolic and one chloroplastic. Mass calibrations on BNE gels showed that the cytosolic GS1 holoenzyme was ~490kDa and likely a dodecamer, and the chloroplastic GS2 holoenzyme was ~240kDa and likely a hexamer. Lastly, our experimental data suggest that the activity of GS isoforms in wheat is regulated by subcellular localization, assembly, and modification to achieve their roles during plant development.« less

Functional Biomaterials: Solution Electrospinning and Gelation of Whey Protein and Pullulan

NASA Astrophysics Data System (ADS)

Sullivan, Stephanie Tolstedt

Utilizing biomaterials that are biodegradable, biocompatible and edible serve well for food products as well as biomedical applications. Biomaterials whey protein and pullulan both have these characteristics. Whey proteins (WP) have been used in food products for many years and more recently in pharmaceutical products. They have the ability to form both gels and stable foams. Pullulan (PULL) has also been used in both food and pharmaceutical products, and is a highly water soluble, non-gelling polysaccharide and has been used primarily as a film former. Herein, we investigate the ability of whey protein and pullulan to form nanofibers and gels. Combining their distinct properties allows the ability to uniquely manipulate nanofiber and gel characteristics and behavior for a variety of applications, from food to even tissue scaffolding. First, we determined the electrospinnability of aqueous whey protein solutions. Both whey protein isolate (WPI) and one of its major components beta--lactoglobulin (BLG), either in native or denatured form, yielded interesting micro and nanostructures when electrosprayed; while nanofiber production required blending with a spinnable polymer, poly(ethylene oxide) (PEO). WP:PEO solutions were also successfully electrospun at acidic pH (2≤pH≤3), which could improve shelf life. Fourier Transform Infrared Reflectance (FTIR) analysis of WP:PEO fiber mat indicated some variation in WP secondary structure with varying WPI concentration (as WPI increased, % alpha-helix increased and beta-turn decreased) and pH (as pH decreased from neutral (7.5) to acidic (2), % beta-sheet decreased and alpha-helix increased). X-ray Photoelectron Spectroscopy (XPS) also confirmed the presence of WP on the surface of the blend fibers, augmenting the FTIR analysis. Interestingly, WP:PEO composite nanofibers maintained its fibrous morphology at temperatures as high as 100 °C, above the 60 °C PEO melting point. Further, we show that the blend mats retained a fibrous structure after the heat treatment. Our second goal was to evaluate the ability of aqueous blends of whey protein and pullulan to form gels. We first looked at WP-PULL blend solutions at room temperature, finding an increasing linear trend in low shear viscosity as the relative concentration of pullulan increased. Blend solution samples were then heated to determine the ability of the blend solutions to form a gelled network. Starting with a homogeneous WP gel, adding PULL, at native mix or alkaline pH, maintained a transparent homogeneous microstructure, but resulted in weaker gels based on its response to stress. At WP isoelectric point (IEP) pH, both protein and blend gels became opaque due to protein aggregation, forming a particulate gel. All gels at the IEP were weaker, yielding at much lower stress and corresponding strain, due to the protein aggregation. The addition of transglutaminase enzyme yielded a stronger network than the native samples, while the addition of sodium trimetaphosphate salt yielded weaker gels and also induced relevant particle and/or course stranded microstructure in both pH 8 and IEP cases. The third part of this study demonstrated the ability of pullulan to form nanofibers in the solution electrospinning process. Aqueous pullulan solutions were able to form defect-free nanofibers with a minimum concentration of 15 w/w%. Pullulan and PULL:hydroxypropyl-beta- cyclodextrin (HPBCD) blend fibers were chemically crosslinked to form insoluble fibers using ethylene glycol diglycidyl ether (EGDGE), a chemical used in food contact coating applications. Next, solution blends of pullulan with whey protein were prepared and also electrospun at varying pH and relative biomaterial concentrations at 17 total w/w%. PULL-WP blend nanofiber mats were crosslinked via heat treatment and found to be both swellable and insoluble. When dried, the mats did not return to their original fiber state and instead appear to be gelatinous fibers in nature after soaking, and thereby making them potentially useful for tissue scaffolding applications. A fourth accomplishment was to utilize Near Infrared Reflectance (NIR) Spectroscopy and Chemometrics techniques to analyze commercial whey protein powder characteristics such as protein, fat and moisture content as well as pH. NIR has been utilized in the food and pharmaceutical industries for quality control as a valuable compliment to or replacement for more expensive testing such as High Performance Liquid Chromatography. Analysis resulted in the development of quantitative, linear regression models to correlate whey protein powder characteristics to NIR data. Whey protein's ability to form gels and pullulan's electrospinnability to form nanofibers is combined herein to form blends of both that can be changed with varying concentration, pH, temperature and supplementation with food-safe additives. The study correlates mechanical properties and microstructure of blend gels and nanofibers and provides a foundation for further study of swellable network for tissue application specifically in the use of pullulan-whey protein heat treated nanofiber mats.

Mitochondrial NADH Fluorescence is Enhanced by Complex I Binding

PubMed Central

Blinova, Ksenia; Levine, Rodney L.; Boja, Emily S.; Griffiths, Gary L.; Shi, Zhen-Dan; Ruddy, Brian; Balaban, Robert S.

2012-01-01

Mitochondrial NADH fluorescence has been a useful tool in evaluating mitochondrial energetics both in vitro and in vivo. Mitochondrial NADH fluorescence is enhanced several fold in the matrix through extended fluorescence lifetimes (EFL). However, the actual binding sites responsible for NADH EFL are unknown. We tested the hypothesis that NADH binding to Complex I is a significant source of mitochondrial NADH fluorescence enhancement. To test this hypothesis, the effect of Complex I binding on NADH fluorescence efficiency was evaluated in purified protein, and in native gels of the entire porcine heart mitochondria proteome. To avoid the oxidation of NADH in these preparations, we conducted the binding experiments under anoxic conditions in a specially designed apparatus. Purified intact Complex I enhanced NADH fluorescence in native gels approximately 10 fold. However, no enhancement was detected in denatured individual Complex I subunit proteins. In the Clear and Ghost native gels of the entire mitochondrial proteome, NADH fluorescence enhancement was localized to regions where NADH oxidation occurred in the presence of oxygen. Inhibitor and mass spectroscopy studies revealed that the fluorescence enhancement was specific to Complex I proteins. No fluorescence enhancement was detected for MDH or other dehydrogenases in this assay system, at physiological mole fractions of the matrix proteins. These data suggest that NADH associated with Complex I significantly contributes to the overall mitochondrial NADH fluorescence signal and provides an explanation for the well established close correlation of mitochondrial NADH fluorescence and the metabolic state. PMID:18702505

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.

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.

Further development of an electroosmotic medium pump system for preparative disk gel electrophoresis.

PubMed

Hayakawa, Mitsuo; Hosogi, Yumiko; Takiguchi, Hisashi; Shiroza, Teruaki; Shibata, Yasuko; Hiratsuka, Koichi; Kiyama-Kishikawa, Michiko; Hamajima, Susumu; Abiko, Yoshimitsu

2003-02-01

A simple and practical 6.8-cm-diameter (36.30-cm(2) cross-sectional-area) preparative disk gel electrophoresis device, based on the design of M. Hayakawa et al. (Anal. Biochem. 288 (2001) 168), in which the elution buffer is driven by an electroosmotic buffer flow through the membrane into the elution chamber from the anode chamber was constructed. We have found that the dialysis membranes employed provide suitable flow rates for the elution buffer, similar to those of an earlier 3.6-cm-diameter device, resulting in the prevention of excess eluate dilution. The efficiency of this device was demonstrated by the fractionation of a bovine serum albumin (BSA) Cohn V fraction into monomer, dimer, and oligomer components using nondenaturing polyacrylamide gel electrophoresis (native-PAGE). The maximum protein concentration of the eluate achieved was 133 mg/ml of BSA monomer, which required a dilution of the eluate for subsequent analytical PAGE performance. As a practical example, the two-dimensional fractionation of soluble dipeptidyl peptidase IV (sDPP IV) from 50 ml fetal bovine serum (3.20 g protein) per gel is presented. The sDPP IV enzyme protein was recovered in a relatively short time, utilizing a 6.5% T native-PAGE and subsequential sodium dodecyl sulfate-PAGE system. This device enhances the possibility of continuous electrophoretic fractionation of complex protein mixtures on a preparative scale. Copyright 2003 Elsevier Science (USA)

The Goat (Capra hircus) Mammary Gland Mitochondrial Proteome: A Study on the Effect of Weight Loss Using Blue-Native PAGE and Two-Dimensional Gel Electrophoresis.

PubMed

Cugno, Graziano; Parreira, José R; Ferlizza, Enea; Hernández-Castellano, Lorenzo E; Carneiro, Mariana; Renaut, Jenny; Castro, Noemí; Arguello, Anastasio; Capote, Juan; Campos, Alexandre M O; Almeida, André M

2016-01-01

Seasonal weight loss (SWL) is the most important limitation to animal production in the Tropical and Mediterranean regions, conditioning producer's incomes and the nutritional status of rural communities. It is of importance to produce strategies to oppose adverse effects of SWL. Breeds that have evolved in harsh climates have acquired tolerance to SWL through selection. Most of the factors determining such ability are related to changes in biochemical pathways as affected by SWL. In this study, a gel based proteomics strategy (BN: Blue-Native Page and 2DE: Two-dimensional gel electrophoresis) was used to characterize the mitochondrial proteome of the secretory tissue of the goat mammary gland. In addition, we have conducted an investigation of the effects of weight loss in two goat breeds with different levels of adaptation to nutritional stress: Majorera (tolerant) and Palmera (susceptible). The study used Majorera and Palmera dairy goats, divided in 4 sets, 2 for each breed: underfed group fed on wheat straw (restricted diet, so their body weight would be 15-20% reduced by the end of experiment), and a control group fed with an energy-balanced diet. At the end of the experimental period (22 days), mammary gland biopsies were obtained for all experimental groups. The proteomic analysis of the mitochondria enabled the resolution of a total of 277 proteins, and 148 (53%) were identified by MALDI-TOF/TOF mass spectrometry. Some of the proteins were identified as subunits of the glutamate dehydrogenase complex and the respiratory complexes I, II, IV, V from mitochondria, as well as numerous other proteins with functions in: metabolism, development, localization, cellular organization and biogenesis, biological regulation, response to stimulus, among others, that were mapped in both BN and 2DE gels. The comparative proteomics analysis enabled the identification of several proteins: NADH-ubiquinone oxidoreductase 75 kDa subunit and lamin B1 mitochondrial (up-regulated in the Palmera breed), Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 (up-regulated in the Majorera breed) and cytochrome b-c1 complex subunit 1, mitochondrial and Chain D, Bovine F1-C8 Sub-Complex Of Atp Synthase (down-regulated in the Majorera breed) as a consequence of weight loss.

The Goat (Capra hircus) Mammary Gland Mitochondrial Proteome: A Study on the Effect of Weight Loss Using Blue-Native PAGE and Two-Dimensional Gel Electrophoresis

PubMed Central

Cugno, Graziano; Parreira, José R.; Ferlizza, Enea; Hernández-Castellano, Lorenzo E.; Carneiro, Mariana; Renaut, Jenny; Castro, Noemí; Arguello, Anastasio; Capote, Juan

2016-01-01

Seasonal weight loss (SWL) is the most important limitation to animal production in the Tropical and Mediterranean regions, conditioning producer’s incomes and the nutritional status of rural communities. It is of importance to produce strategies to oppose adverse effects of SWL. Breeds that have evolved in harsh climates have acquired tolerance to SWL through selection. Most of the factors determining such ability are related to changes in biochemical pathways as affected by SWL. In this study, a gel based proteomics strategy (BN: Blue-Native Page and 2DE: Two-dimensional gel electrophoresis) was used to characterize the mitochondrial proteome of the secretory tissue of the goat mammary gland. In addition, we have conducted an investigation of the effects of weight loss in two goat breeds with different levels of adaptation to nutritional stress: Majorera (tolerant) and Palmera (susceptible). The study used Majorera and Palmera dairy goats, divided in 4 sets, 2 for each breed: underfed group fed on wheat straw (restricted diet, so their body weight would be 15–20% reduced by the end of experiment), and a control group fed with an energy-balanced diet. At the end of the experimental period (22 days), mammary gland biopsies were obtained for all experimental groups. The proteomic analysis of the mitochondria enabled the resolution of a total of 277 proteins, and 148 (53%) were identified by MALDI-TOF/TOF mass spectrometry. Some of the proteins were identified as subunits of the glutamate dehydrogenase complex and the respiratory complexes I, II, IV, V from mitochondria, as well as numerous other proteins with functions in: metabolism, development, localization, cellular organization and biogenesis, biological regulation, response to stimulus, among others, that were mapped in both BN and 2DE gels. The comparative proteomics analysis enabled the identification of several proteins: NADH-ubiquinone oxidoreductase 75 kDa subunit and lamin B1 mitochondrial (up-regulated in the Palmera breed), Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 (up-regulated in the Majorera breed) and cytochrome b-c1 complex subunit 1, mitochondrial and Chain D, Bovine F1-C8 Sub-Complex Of Atp Synthase (down-regulated in the Majorera breed) as a consequence of weight loss. PMID:27031334

The belonging of gpMuc, a glycoprotein from Mucuna pruriens seeds, to the Kunitz-type trypsin inhibitor family explains its direct anti-snake venom activity.

PubMed

Scirè, Andrea; Tanfani, Fabio; Bertoli, Enrico; Furlani, Emiliano; Nadozie, Hope-Onyekwere N; Cerutti, Helena; Cortelazzo, Alessio; Bini, Luca; Guerranti, Roberto

2011-07-15

In Nigeria, Mucuna pruriens seeds are locally prescribed as an oral prophylactic for snake bite and it is claimed that when two seeds are swallowed they protect the individual for a year against snake bites. In order to understand the Mucuna pruriens antisnake properties, the proteins from the acqueous extract of seeds were purified by three chromatographic steps: ConA affinity chromatography, tandem anionic-cationic exchange and gel filtration, obtaining a fraction conventionally called gpMucB. This purified fraction was analysed by SDS-PAGE obtaining 3 bands with apparent masses ranging from 20 to 24 kDa, and by MALDI-TOF which showed two main peaks of 21 and 23 kDa and another small peak of 19 kDa. On the other hand, gel filtration analysis of the native protein indicated a molecular mass of about 70 kDa suggesting that in its native form, gpMucB is most likely an oligomeric multiform protein. Infrared spectroscopy of gpMucB indicated that the protein is particularly thermostable both at neutral and acidic pHs and that it is an all beta protein. All data suggest that gpMucB belongs to the Kunitz-type trypsin inhibitor family explaining the direct anti-snake venom activity of Mucuna pruriens seeds. Copyright © 2011 Elsevier GmbH. All rights reserved.

Cellular localization and detergent dependent oligomerization of rice allene oxide synthase-1.

PubMed

Yoeun, Sereyvath; Kim, Jeong-Il; Han, Oksoo

2015-01-01

Allene oxide synthase-1 from Oryza sativa (OsAOS1) localizes to the chloroplast, but lacks a putative chloroplast targeting sequence typically found in dicot AOS. Here, kinetic parameters and the oligomerization state/subunit composition of OsAOS1 were characterized in vitro in the absence or presence of detergent micelles. The catalytic efficiency (k(cat)/K(m)) of OsAOS1 reached a maximum near the critical micelle concentration for polyoxyethylene 10 tridecyl ether. Native gel analysis showed that OsAOS1 exists as a multimer in the absence of detergent micelles. The multimeric form of OsAOS1 was stably cross-linked in the absence of detergents, while only monomeric OsAOS1 was detected in the presence of detergent micelles. Gel filtration analysis indicated that the oligomeric state of OsAOS1 depends strongly on the detergents and that the monomer becomes the predominant form in the presence of detergent micelles. These data suggest that the detergent-dependent oligomeric state of OsAOS1 is an important factor for the regulation of its catalytic efficiency.

A streamlined isolation method and the autoxidation profiles of tuna myoglobin.

PubMed

Nurilmala, Mala; Ushio, Hideki; Watabe, Shugo; Ochiai, Yoshihiro

2018-05-01

Determination of the redox state of myoglobin (Mb) gives useful information for evaluating the quality of tuna meat. To attain this purpose, a fast streamlined method has been established basically based on preparative native gel electrophoresis to isolate Mb from the dark muscle of Pacific bluefin tuna. Crude Mb fraction was prepared from dark muscle by ammonium sulfate saturation fractionation and subsequently Mb was purified by preparative native gel electrophoresis under the isoelectric pH of the Mb, resulting in absorption (or trapping) of all the contaminating proteins in the gel. Purified Mb was converted to oxy form with a trace amount of sodium hydrosulfite, and subsequently dialyzed against 50 mM sodium citrate (pH 5.6) or 50 mM sodium phosphate (pH 6.5). The purified tuna Mb was examined for the temperature and pH dependencies of autoxidation using horse Mb as a reference. Tuna Mb was oxidized 2.5-3 times faster than horse Mb irrespective of the pH conditions examined. The highest autoxidation rates both at 0 and 37 °C were observed at pH 5.6. These data were comparable to those obtained for Mbs isolated by conventional chromatographic methods.

Detection of platinum species in plant material.

PubMed

Messerschmidt, J; Alt, F; Tölg, G

1995-05-01

Model experiments for the detection of platinum species in extracts from native and platinum-treated grass cultivations are described. The procedural steps are cultivation of the grass samples, extraction and concentration of the platinum species by ultrafiltration and freeze-drying, preparative separation of the species by gel chromatography followed by isotachophoresis, and sequential analytical detection of the separated platinum species by adsorptive voltammetry. After isotachophoresis, sharp peaks of platinum species could be detected. In the native grass extract only one platinum species (160-200 kDa) was found. In the platinum-treated grass extracts several platinum species were observed in the molecular mass range from 1 to > 1000 kDa. By an extremely sensitive platinum determination method (adsorptive voltammetry; detection limit, 2 pg Pt abs.) it was possible to detect platinum even in stained protein bands from horizontal gel electrophoresis of platinum containing fractions obtained after isotachophoresis.

Multiple forms of ADP-glucose pyrophosphorylase from tomato fruit

NASA Technical Reports Server (NTRS)

Chen, B. Y.; Janes, H. W.

1997-01-01

ADP-glucose pyrophosphorylase (AGP) was purified from tomato (Lycopersicon esculentum Mill.) fruit to apparent homogeneity. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis the enzyme migrated as two close bands with molecular weights of 50,000 and 51,000. Two-dimensional polyacrylamide gel electrophoresis analysis of the purified enzyme, however, revealed at least five major protein spots that could be distinguished by their slight differences in net charge and molecular weight. Whereas all of the spots were recognized by the antiserum raised against tomato fruit AGP holoenzyme, only three of them reacted strongly with antiserum raised against the potato tuber AGP large subunit, and the other two spots (with lower molecular weights) reacted specifically with antisera raised against spinach leaf AGP holoenzyme and the potato tuber AGP small subunit. The results suggest the existence of at least three isoforms of the AGP large subunit and two isoforms of the small subunit in tomato fruit in vivo. The native molecular mass of the enzyme determined by gel filtration was 220 +/- 10 kD, indicating a tetrameric structure for AGP from tomato fruit. The purified enzyme is very sensitive to 3-phosphoglycerate/inorganic phosphate regulation.

Highly porous ceramic oxide aerogels having improved flexibility

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor); Nguyen, Baochau N. (Inventor)

2012-01-01

Ceramic oxide aerogels incorporating periodically dispersed flexible linkages are provided. The flexible linkages impart greater flexibility than the native aerogels without those linkages, and have been shown to reduce or eliminate the need for supercritical CO.sub.2-mediated drying of the corresponding wet gels. The gels may also be polymer cross-linked via organic polymer chains that are attached to and extend from surface-bound functional groups provided or present over the internal surfaces of a mesoporous ceramic oxide particle network via appropriate chemical reactions.

Collagen telopeptides (cross-linking sites) play a role in collagen gel lattice contraction

NASA Technical Reports Server (NTRS)

Woodley, D. T.; Yamauchi, M.; Wynn, K. C.; Mechanic, G.; Briggaman, R. A.

1991-01-01

Solubilized interstitial collagens will form a fibrillar, gel-like lattice when brought to physiologic conditions. In the presence of human dermal fibroblasts the collagen lattice will contract. The rate of contraction can be determined by computer-assisted planemetry. The mechanisms involved in contraction are as yet unknown. Using this system it was found that the rate of contraction was markedly decreased when collagen lacking telopeptides was substituted for native collagen. Histidinohydroxylysinonorleucine (HHL) is a major stable trifunctional collagen cross-link in mature skin that involves a carboxyl terminal, telopeptide site 16c, the sixteenth amino acid residue from the carboxy terminal of the telopeptide region of alpha 1 (I) in type I collagen. Little, if any, HHL was present in native, purified, reconstituted, soluble collagen fibrils from 1% acetic acid-extracted 2-year-old bovine skin. In contrast, HHL cross-links were present (0.22 moles of cross-link per mole of collagen) in lattices of the same collagen contracted by fibroblasts. However, rat tail tendon does not contain HHL cross-links, and collagen lattices made of rat tail tendon collagen are capable of contraction. This suggests that telopeptide sites, and not mature HHL cross-links per se, are essential for fibroblasts to contract collagen lattices. Beta-aminopropionitrile fumarate (BAPN), a potent lathyrogen that perturbs collagen cross-linking by inhibition of lysyl oxidase, also inhibited the rate of lattice cell contraction in lattices composed of native collagen. However, the concentrations of BAPN that were necessary to inhibit the contraction of collagen lattices also inhibited fibroblast growth suggestive of cellular toxicity. In accordance with other studies, we found no inhibition of the rate of lattice contraction when fibronectin-depleted serum was used. Electron microscopy of contracted gels revealed typical collagen fibers with a characteristic axial periodicity. The data provide evidence that collagen telopeptide sites play a role in collagen gel lattice contraction.

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

PubMed

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

2007-12-01

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

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

PubMed Central

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

2007-01-01

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

Effects of pH-Shift Processing and Microbial Transglutaminase on the Gel and Emulsion Characteristics of Porcine Myofibrillar System

PubMed Central

Hong, Geun-Pyo; Chun, Ji-Yeon; Jo, Yeon-Ji

2014-01-01

This study investigated the effects of microbial transglutaminase (MTGase) and pH-shift processing on the functional properties of porcine myofibrillar proteins (MP). The pH-shift processing was carried out by decreasing the pH of MP suspension to 3.0, followed by re-adjustment to pH 6.2. The native (CM) and pH-shifted MP (PM) was reacted with and without MTGase, and the gelling and emulsion characteristics were compared. To compare the pH-shifted MTGase-treated MP (PT), deamidation (DM) was conducted by reacting MTGase with MP at pH 3.0. Rigid thermal gel was produced by MTGase-treated native MP (CT) and PT. PM and DM showed the lowest storage modulus (G') at the end of thermal scanning. Both MTGase and pH-shifting produced harder MP gel, and the highest gel strength was obtained in PT. All treatments yielded lower than CM, and CT showed significantly higher yield than PM and DM treatments. For emulsion characteristics, pH-shifting improved the emulsifying ability of MP-stabilized emulsion, while the treatments had lower emulsion stability. PM-stabilized emulsion exhibited the lowest creaming stability among all treatments. The emulsion stability could be improved by the usage of MTGase. The results indicated that pH-shifting combined with MTGase had a potential application to modify or improve functional properties of MP in manufacturing of meat products. PMID:26760940

Structural modification of swai-fish (Pangasius hypophthalmus)-based emulsions containing non-meat protein additives by ultra-high pressure and thermal treatments

NASA Astrophysics Data System (ADS)

Techarang, Jiranat; Apichartsrangkoon, Arunee; Phanchaisri, Boonrak; Pathomrungsiyoungkul, Pattavara; Sriwattana, Sujinda

2017-07-01

Swai-fish emulsions containing fermented soybeans (thua nao and rice-koji miso) were pressurized at 600 MPa for 20 min or heated at 72°C for 30 min. The fish batters were blended with soy protein isolate (SPI) or whey protein concentrate (WPC) to stabilize the emulsions. The processed fish emulsions were then subjected to physical, chemical and microbiological examinations. The results of gel strength and water-holding potential showed that SPI addition yielded higher impact on these properties than WPC addition, which was also confirmed by the interactions between SPI and native fish proteins depicted by electrophoregrams. The frequency profiles suggested that the heated gels had a greater storage and loss moduli than pressurized gels, while pressurized WPC set-gel displayed larger loss tangent (the predominance of viscous moiety) than those pressurized SPI set-gel. High bacteria and spore counts of B. subtilis (residual of the thua nao) were observed in both pressurized and heated fish-based emulsions.

Bacillus pumilus ES4: candidate plant growth-promoting bacterium to enhance establishment of plants in mine tailings

PubMed Central

de-Bashan, Luz E.; Hernandez, Juan-Pablo; Bashan, Yoav; Maier, Raina

2014-01-01

Three plant growth-promoting bacteria (PGPB; Bacillus pumilus ES4, B. pumilus RIZO1, and Azospirillum brasilense Cd) were tested for their ability to enhance plant growth and development of the native Sonoran Desert shrub quailbush (Atriplex lentiformis) and for their effect on the native bacterial community in moderately acidic, high-metal content (AHMT) and in neutral, low metal content natural tailings (NLMT) in controlled greenhouse experiments. Inoculation of quailbush with all three PGPB significantly enhanced plant growth parameters, such as germination, root length, dry weight of shoots and roots, and root/shoot ratio in both types of tailings. The effect of inoculation on the indigenous bacterial community by the most successful PGPB Bacillus pumilus ES4 was evaluated by denaturating gradient gel electrophoresis (PCR-DGGE) fingerprinting and root colonization was followed by specific fluorescent in situ hybridization (FISH). Inoculation with this strain significantly changed the bacterial community over a period of 60 days. FISH analysis showed that the preferred site of colonization was the root tips and root elongation area. This study shows that inoculation of native perennial plants with PGPB can be used for developing technologies for phytostabilizing mine tailings. PMID:25009362

Prospection and Evaluation of (Hemi) Cellulolytic Enzymes Using Untreated and Pretreated Biomasses in Two Argentinean Native Termites

PubMed Central

Ben Guerrero, Emiliano; Arneodo, Joel; Bombarda Campanha, Raquel; Abrão de Oliveira, Patrícia; Veneziano Labate, Mônica T.; Regiani Cataldi, Thaís; Campos, Eleonora; Cataldi, Angel; Labate, Carlos A.; Martins Rodrigues, Clenilson; Talia, Paola

2015-01-01

Saccharum officinarum bagasse (common name: sugarcane bagasse) and Pennisetum purpureum (also known as Napier grass) are among the most promising feedstocks for bioethanol production in Argentina and Brazil. In this study, both biomasses were assessed before and after acid pretreatment and following hydrolysis with Nasutitermes aquilinus and Cortaritermes fulviceps termite gut digestome. The chemical composition analysis of the biomasses after diluted acid pretreatment showed that the hemicellulose fraction was partially removed. The (hemi) cellulolytic activities were evaluated in bacterial culture supernatants of termite gut homogenates grown in treated and untreated biomasses. In all cases, we detected significantly higher endoglucanase and xylanase activities using pretreated biomasses compared to untreated biomasses, carboxymethylcellulose and xylan. Several protein bands with (hemi) cellulolytic activity were detected in zymograms and two-dimensional gel electrophoresis. Some proteins of these bands or spots were identified as xylanolytic peptides by mass spectrometry. Finally, the diversity of cultured cellulolytic bacterial endosymbionts associated to both Argentinean native termite species was analyzed. This study describes, for the first time, bacterial endosymbionts and endogenous (hemi) cellulases of two Argentinean native termites as well as their potential application in degradation of lignocellulosic biomass for bioethanol production. PMID:26313257

Osteochondral Biopsy Analysis Demonstrates That BST-CarGel Treatment Improves Structural and Cellular Characteristics of Cartilage Repair Tissue Compared With Microfracture

PubMed Central

Méthot, Stéphane; Changoor, Adele; Tran-Khanh, Nicolas; Hoemann, Caroline D.; Stanish, William D.; Restrepo, Alberto; Shive, Matthew S.; Buschmann, Michael D.

2016-01-01

Objective The efficacy and safety of BST-CarGel, a chitosan-based medical device for cartilage repair, was compared with microfracture alone at 1 year during a multicenter randomized controlled trial (RCT) in the knee. The quality of repair tissue of osteochondral biopsies collected from a subset of patients was compared using blinded histological assessments. Methods The international RCT evaluated repair tissue quantity and quality by 3-dimensional quantitative magnetic resonance imaging as co-primary endpoints at 12 months. At an average of 13 months posttreatment, 21/41 BST-CarGel and 17/39 microfracture patients underwent elective second look arthroscopies as a tertiary endpoint, during which ICRS (International Cartilage Repair Society) macroscopic scoring was carried out, and osteochondral biopsies were collected. Stained histological sections were evaluated by blinded readers using ICRS I and II histological scoring systems. Collagen organization was evaluated using a polarized light microscopy score. Results BST-CarGel treatment resulted in significantly better ICRS macroscopic scores (P = 0.0002) compared with microfracture alone, indicating better filling, integration, and tissue appearance. Histologically, BST-CarGel resulted in a significant improvement of structural parameters—Surface Architecture (P = 0.007) and Surface/Superficial Assessment (P = 0.042)—as well as cellular parameters—Cell Viability (P = 0.006) and Cell Distribution (P = 0.032). No histological parameters were significantly better for the microfracture group. BST-CarGel treatment also resulted in a more organized repair tissue with collagen stratification more similar to native hyaline cartilage, as measured by polarized light microscopy scoring (P = 0.0003). Conclusion Multiple and independent analyses in this biopsy substudy demonstrated that BST-CarGel treatment results in improved structural and cellular characteristics of repair tissue at 1 year posttreatment compared with microfracture alone, supporting previously reported results by quantitative magnetic resonance imaging. PMID:26958314

Spectroscopic chemical analysis methods and apparatus

NASA Technical Reports Server (NTRS)

Hug, William F. (Inventor); Reid, Ray D. (Inventor)

2009-01-01

Spectroscopic chemical analysis methods and apparatus are disclosed which employ deep ultraviolet (e.g. in the 200 nm to 300 nm spectral range) electron beam pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor light emitting devices, and hollow cathode metal ion lasers to perform non-contact, non-invasive detection of unknown chemical analytes. These deep ultraviolet sources enable dramatic size, weight and power consumption reductions of chemical analysis instruments. Chemical analysis instruments employed in some embodiments include capillary and gel plane electrophoresis, capillary electrochromatography, high performance liquid chromatography, flow cytometry, flow cells for liquids and aerosols, and surface detection instruments. In some embodiments, Raman spectroscopic detection methods and apparatus use ultra-narrow-band angle tuning filters, acousto-optic tuning filters, and temperature tuned filters to enable ultra-miniature analyzers for chemical identification. In some embodiments Raman analysis is conducted simultaneously with native fluorescence spectroscopy to provide high levels of sensitivity and specificity in the same instrument.

Spectroscopic chemical analysis methods and apparatus

NASA Technical Reports Server (NTRS)

Reid, Ray D. (Inventor); Hug, William F. (Inventor)

2010-01-01

Spectroscopic chemical analysis methods and apparatus are disclosed which employ deep ultraviolet (e.g. in the 200 nm to 300 nm spectral range) electron beam pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor light emitting devices, and hollow cathode metal ion lasers to perform non-contact, non-invasive detection of unknown chemical analytes. These deep ultraviolet sources enable dramatic size, weight and power consumption reductions of chemical analysis instruments. Chemical analysis instruments employed in some embodiments include capillary and gel plane electrophoresis, capillary electrochromatography, high performance liquid chromatography, flow cytometry, flow cells for liquids and aerosols, and surface detection instruments. In some embodiments, Raman spectroscopic detection methods and apparatus use ultra-narrow-band angle tuning filters, acousto-optic tuning filters, and temperature tuned filters to enable ultra-miniature analyzers for chemical identification. In some embodiments Raman analysis is conducted simultaneously with native fluorescence spectroscopy to provide high levels of sensitivity and specificity in the same instrument.

Sea spray aerosol structure and composition using cryogenic transmission electron microscopy

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

Patterson, Joseph P.; Collins, Douglas B.; Michaud, Jennifer M.

The surface properties of atmospheric aerosol particles largely control their impact on climate by affecting their ability to uptake water, react heterogeneously, and nucleate ice in clouds. However, in the vacuum of a conventional electron microscope, the native surface structure often undergoes chemical rearrangement resulting in surfaces that are quite different from their atmospheric configurations. Herein, we report the development of a cryo-TEM approach where sea spray aerosol particles are flash frozen in their native state and then probed by electron microscopy. This unique approach allows for the detection of not only mixed salts, but also soft materials including wholemore » hydrated bacteria, diatoms, virus particles, marine vesicles, as well as gel networks within hydrated salt droplets. As a result, we anticipate this method will open up a new avenue of analysis for aerosol particles, not only for ocean-derived aerosols, but for those produced from other sources where there is interest in the transfer of organic or biological species from the biosphere to the atmosphere.« less

Sea spray aerosol structure and composition using cryogenic transmission electron microscopy

DOE PAGES

Patterson, Joseph P.; Collins, Douglas B.; Michaud, Jennifer M.; ...

2016-01-15

The surface properties of atmospheric aerosol particles largely control their impact on climate by affecting their ability to uptake water, react heterogeneously, and nucleate ice in clouds. However, in the vacuum of a conventional electron microscope, the native surface structure often undergoes chemical rearrangement resulting in surfaces that are quite different from their atmospheric configurations. Herein, we report the development of a cryo-TEM approach where sea spray aerosol particles are flash frozen in their native state and then probed by electron microscopy. This unique approach allows for the detection of not only mixed salts, but also soft materials including wholemore » hydrated bacteria, diatoms, virus particles, marine vesicles, as well as gel networks within hydrated salt droplets. As a result, we anticipate this method will open up a new avenue of analysis for aerosol particles, not only for ocean-derived aerosols, but for those produced from other sources where there is interest in the transfer of organic or biological species from the biosphere to the atmosphere.« less

A model of EcoRII restriction endonuclease action: the active complex is most likely formed by one protein subunit and one DNA recognition site

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Kubareva, E. A.; Shabarova, Z. A.

1999-01-01

To elucidate the mechanism of interaction of restriction endonuclease EcoRII with DNA, we studied by native gel electrophoresis the binding of this endonuclease to a set of synthetic DNA-duplexes containing the modified or canonical recognition sequence 5'-d(CCA/TGG)-3'. All binding substrate or substrate analogues tested could be divided into two major groups: (i) duplexes that, at the interaction with endonuclease EcoRII, form two types of stable complexes on native gel in the absence of Mg2+ cofactor; (ii) duplexes that form only one type of complex, observed both in the presence and absence of Mg2+. Unlike the latter, duplexes under the first group can be hydrolyzed by endonuclease. Data obtained suggest that the active complex is most likely formed by one protein subunit and one DNA recognition sequence. A model of EcoRII endonuclease action is presented.

XPC and human homologs of RAD23: intracellular localization and relationship to other nucleotide excision repair complexes.

PubMed Central

van der Spek, P J; Eker, A; Rademakers, S; Visser, C; Sugasawa, K; Masutani, C; Hanaoka, F; Bootsma, D; Hoeijmakers, J H

1996-01-01

The xeroderma pigmentosum syndrome complementation group C (XP-C) is due to a defect in the global genome repair subpathway of nucleotide excision repair (NER). The XPC protein is complexed with HHR23B, one of the two human homologs of the yeast NER protein, RAD23 (Masutani at al. (1994) EMBO J. 8, 1831-1843). Using heparin chromatography, gel filtration and native gel electrophoresis we demonstrate that the majority of HHR23B is in a free, non-complexed form, and that a minor fraction is tightly associated with XPC. In contrast, we cannot detect any bound HHR23A. Thus the HHR23 proteins may have an additional function independent of XPC. The fractionation behaviour suggests that the non-bound forms of the HHR23 proteins are not necessary for the core of the NER reaction. Although both HHR23 proteins share a high level of overall homology, they migrate very differently on native gels, pointing to a difference in conformation. Gel filtration suggests the XPC-HHR23B heterodimer resides in a high MW complex. However, immunodepletion studies starting from repair-competent Manley extracts fall to reveal a stable association of a significant fraction of the HHR23 proteins or the XPC-HHR23B complex with the basal transcription/repair factor TFIIH, or with the ERCC1 repair complex. Consistent with a function in repair or DNA/chromatin metabolism, immunofluorescence studies show all XPC, HHR23B and (the free) HHR23A to reside in the nucleus. PMID:8692695

Development of oxidised and heat-moisture treated potato starch film.

PubMed

Zavareze, Elessandra da Rosa; Pinto, Vânia Zanella; Klein, Bruna; El Halal, Shanise Lisie Mello; Elias, Moacir Cardoso; Prentice-Hernández, Carlos; Dias, Alvaro Renato Guerra

2012-05-01

This study investigated the effects of sodium hypochlorite oxidation and a heat-moisture treatment of potato starch on the physicochemical, pasting and textural properties of potato starches in addition to the water vapour permeability (WVP) and mechanical properties of potato starch films produced from these starches. The carbonyl contents, carboxyl contents, swelling power, solubility, pasting properties and gel texture of the native, oxidised and heat-moisture treated (HMT) starches were evaluated. The films made of native, oxidised and HMT starches were characterised by thickness, water solubility, colour, opacity, mechanical properties and WVP. The oxidised and HMT starches had lower viscosity and swelling power compared to the native starch. The films produced from oxidised potato starch had decreased solubility, elongation and WVP values in addition to increased tensile strength compared to the native starch films. The HMT starch increased the tensile strength and WVP of the starch films compared to the native starch. Copyright © 2011 Elsevier Ltd. All rights reserved.

Purification and properties of aryl acylamidase from Pseudomonas fluorescens ATCC 39004.

PubMed

Hammond, P M; Price, C P; Scawen, M D

1983-05-16

Aryl acylamidase has been purified from a strain of Pseudomonas fluorescens ATCC 39004, selected from soil on the basis of its ability to utilise acylanilide compounds as a sole source of carbon. The enzyme was purified to homogeneity by a combination of ion-exchange, hydrophobic and gel-permeation chromatography. A relative molecular mass of about 52 500 was estimated by gel filtration. The native enzyme was shown to be a monomeric protein by sodium dodecyl sulphate/polyacrylamide gel electrophoresis. The enzyme was maximally active at a pH of 8.6 and at a temperature of 45 degrees C. The enzyme shows Michaelis-Menten kinetics; Km values for nitroacetanilide (69 microM) and hydroxyacetanilide (6.1 microM) were low, indicating that the enzyme has a very high affinity for both substrates.

Purification and properties of trimethylamine oxide reductase from Salmonella typhimurium.

PubMed Central

Kwan, H S; Barrett, E L

1983-01-01

The major inducible trimethylamine oxide reductase was purified from Salmonella typhimurium LT2. The molecular weights of the native enzyme were estimated to be 332,000 by gel filtration and 170,000 by nondenaturing disc gel electrophoresis. In sodium dodecyl sulfate-gel electrophoresis, the enzyme formed a single band of molecular weight 84,000. The isoelectric point was 4.28. Maximum activity was at pH 5.65 and 45 degrees C. Reduced flavin mononucleotide, but not reduced flavin adenine dinucleotide, served as an electron donor. The Km for trimethylamine oxide was 0.89 mM and Vmax was 1,450 U/mg of protein. The enzyme reduced chlorate with a Km of 2.2 mM and a Vmax of 350 U/mg of protein. Images PMID:6350272

Characterization of the stability and folding of H2A.Z chromatin particles: implications for transcriptional activation.

PubMed

Abbott, D W; Ivanova, V S; Wang, X; Bonner, W M; Ausió, J

2001-11-09

H2A.Z and H2A.1 nucleosome core particles and oligonucleosome arrays were obtained using recombinant versions of these histones and a native histone H2B/H3/H4 complement reconstituted onto appropriate DNA templates. Analysis of the reconstituted nucleosome core particles using native polyacrylamide gel electrophoresis and DNase I footprinting showed that H2A.Z nucleosome core particles were almost structurally indistinguishable from its H2A.1 or native chicken erythrocyte counterparts. While this result is in good agreement with the recently published crystallographic structure of the H2A.Z nucleosome core particle (Suto, R. K., Clarkson, M J., Tremethick, D. J., and Luger, K. (2000) Nat. Struct. Biol. 7, 1121-1124), the ionic strength dependence of the sedimentation coefficient of these particles exhibits a substantial destabilization, which is most likely the result of the histone H2A.Z-H2B dimer binding less tightly to the nucleosome. Analytical ultracentrifuge analysis of the H2A.Z 208-12, a DNA template consisting of 12 tandem repeats of a 208-base pair sequence derived from the sea urchin Lytechinus variegatus 5 S rRNA gene, reconstituted oligonucleosome complexes in the absence of histone H1 shows that their NaCl-dependent folding ability is significantly reduced. These results support the notion that the histone H2A.Z variant may play a chromatin-destabilizing role, which may be important for transcriptional activation.

Preparation of mesoporous silica microparticles by sol-gel/emulsion route for protein release.

PubMed

Vlasenkova, Mariya I; Dolinina, Ekaterina S; Parfenyuk, Elena V

2018-04-06

Encapsulation of therapeutic proteins into particles from appropriate material can improve both stability and delivery of the drugs, and the obtained particles can serve as a platform for development of their new oral formulations. The main goal of this work was development of sol-gel/emulsion method for preparation of silica microcapsules capable of controlled release of encapsulated protein without loss of its native structure. For this purpose, the reported in literature direct sol-gel/W/O/W emulsion method of protein encapsulation was used with some modifications, because the original method did not allow to prepare silica microcapsules capable for protein release. The particles were synthesized using sodium silicate and tetraethoxysilane as silica precursors and different compositions of oil phase. In vitro kinetics of bovine serum albumin (BSA) release in buffer (pH 7.4) was studied by Fourier transform infrared (FTIR) and fluorescence spectrometry, respectively. Structural state of encapsulated BSA and after release was evaluated. It was found that the synthesis conditions influenced substantially the porous structure of the unloaded silica particles, release properties of the BSA-loaded silica particles and structural state of the encapsulated and released protein. The modified synthesis conditions made it possible to obtain the silica particles capable of controlled release of the protein during a week without loss of the protein native structure.

Therapeutic potential of gel-based injectables for vocal fold regeneration

PubMed Central

Bartlett, Rebecca S.; Thibeault, Susan L.; Prestwich, Glenn D.

2012-01-01

Vocal folds are anatomically and biomechanically unique, thus complicating the design and implementation of tissue engineering strategies for repair and regeneration. Integration of an enhanced understanding of tissue biomechanics, wound healing dynamics and innovative gel-based therapeutics has generated enthusiasm for the notion that an efficacious treatment for vocal fold scarring could be clinically attainable within several years. Fibroblast phenotype and gene expression are mediated by the three-dimensional mechanical and chemical microenvironment at an injury site. Thus, therapeutic approaches need to coordinate spatial and temporal aspects of the wound healing response in an injured vocal tissue to achieve an optimal clinical outcome. Successful gel-based injectables for vocal fold scarring will require a keen understanding of how the native inflammatory response sets into motion the later extracellular matrix remodeling, which in turn will determine the ultimate biomechanical properties of the tissue. We present an overview of the challenges associated with this translation as well as the proposed gel-based injectable solutions. PMID:22456756

Enzymatically active biomimetic micropropellers for the penetration of mucin gels

PubMed Central

Walker, Debora; Käsdorf, Benjamin T.; Jeong, Hyeon-Ho; Lieleg, Oliver; Fischer, Peer

2015-01-01

In the body, mucus provides an important defense mechanism by limiting the penetration of pathogens. It is therefore also a major obstacle for the efficient delivery of particle-based drug carriers. The acidic stomach lining in particular is difficult to overcome because mucin glycoproteins form viscoelastic gels under acidic conditions. The bacterium Helicobacter pylori has developed a strategy to overcome the mucus barrier by producing the enzyme urease, which locally raises the pH and consequently liquefies the mucus. This allows the bacteria to swim through mucus and to reach the epithelial surface. We present an artificial system of reactive magnetic micropropellers that mimic this strategy to move through gastric mucin gels by making use of surface-immobilized urease. The results demonstrate the validity of this biomimetic approach to penetrate biological gels, and show that externally propelled microstructures can actively and reversibly manipulate the physical state of their surroundings, suggesting that such particles could potentially penetrate native mucus. PMID:26824056

Preparation of intact monomeric collagen from rat tail tendon and skin and the structure of the nonhelical ends in solution.

PubMed

Chandrakasan, G; Torchia, D A; Piez, K A

1976-10-10

Procedures for the preparation of soluble collagen from rat skin and tail tendon were reviewed and revised to permit the preparation of native monomeric collagen with intact nonhelical ends. The degree of intactness was estimated from the tyrosine content, which is present only in the nonhelical ends, and by mobility of the COOH-terminal cyanogen bromide peptide of the alpha1 chain on sodium dodecyl sulfate gels. The amount of covalently cross-linked polymeric material present was estimated by molecular sieve chromatography of denatured samples. Rapid purification in the cold was sufficient to prevent or greatly reduce proteolytic alteration. Fractionation by salt precipitation at acid pH was effective in reducing the content of polymeric material. Rat tail tendon yielded completely intact native collagen, but some high molecular weight aggregates remained. Collagen from the skin of lathyritic rats was easier to obtain free of aggregates, but contained about 1 less tyrosine residue per alpha1 chain even when isolated in the presence of enzyme inhibitors. Proton NMR spectra of denatured acidic solutions of these preparations showed that 4 to 5 tyrosine residues per alpha chain were present, confirming the chemical analysis. Spectra of the native molecule showed that about the same number of tyrosine residues per chain are in rapid motion, unlike residues in the helical portion of the molecule, a result which shows that the nonhelical ends of the native molecule are unstructured in acidic solution.

Biophysical determinants of toluene diisocyanate antigenicity associated with exposure and asthma.

PubMed

Ye, Young-Min; Kim, Cheol-Woo; Kim, Hyung-Ryul; Kim, Hyun-Mi; Suh, Chang-Hee; Nahm, Dong-Ho; Park, Hae-Sim; Redlich, Carrie A; Wisnewski, Adam V

2006-10-01

Toluene diisocyanate (TDI), a widely used aromatic diisocyanate with the potential to cause asthma, reacts with albumin in the airway fluid, which acts as a carrier protein for chemical presentation to the immune system. Structural elucidation of TDI-albumin conjugates is crucial to understanding the human immune response to TDI exposure. Investigate the dependence of TDI's antigenicity on the biophysics of exposure and its association with TDI asthma. Toluene diisocyanate-albumin conjugates were generated by exposing albumin to TDI in liquid or vapor phase (liquid or vapor TDI-albumin, respectively). Conjugates were characterized by native gel electrophoresis and matrix-assisted laser desorption/ionization-mass spectrometry, and used as antigens in ELISA assays for serum specific-IgE and IgG. The physical phase of TDI (vapor vs liquid) affects the formation of TDI-albumin conjugates, with measurable differences in the amount of TDI per albumin molecule, migration in native gels, matrix-assisted laser desorption/ionization-mass spectrometry mass/charge spectra, and antigenicity. Vapor TDI-albumin conjugates were recognized by IgE from 44% of subjects with TDI asthma, whereas liquid TDI-albumin conjugates are recognized by IgE from only 17% of these patients. A significant (P < .05) association between TDI exposure and vapor TDI-albumin specific serum IgG was also observed. Biophysics of TDI exposure substantially affects formation of TDI-albumin conjugates recognized by the immune system in association with exposure and asthma. The data suggest that serology may help identify TDI asthmatics and exposed workers if the appropriate form of TDI is used as the antigenic basis for analysis.

Thiolated citrus low-methoxyl pectin: Synthesis, characterization and rheological and oxidation-responsive gelling properties.

PubMed

Chen, Jinfeng; Ye, Fayin; Zhou, Yun; Zhao, Guohua

2018-02-01

In the present study, citrus low-methoxyl pectin was modified by conjugating cysteine via amide bonds, and the resultant polymer (CYS-PEC) was characterized. CYS-PEC conjugates with thiol contents varying from 77.8μmol/g to 296μmol/g were synthesized, and the successful conjugation was evidenced by elemental, and FT-IR analyses. The sulfur in CYS-PEC is predominately in the thiol form, with a minor fraction forming disulfide bonds (∼15%), which occur when thiol/disulfide interchange interrupts the intended thiolation. Both native and modified pectin dispersions exhibited strong pseudoplastic properties, and the frequency sweeps revealed them to be dispersions containing microgel particles. Dynamic viscoelastic analysis was used to determine the oxidation-response gelling capacities of polymer dispersions containing H 2 O 2 , especially those that are highly thiolated and have cross-linked gel properties. For oxidation-induced CYS-PEC gels, their gelation time, hardness, viscosity and elastic moduli and swelling-disintegration ratio are dependent on the thiol group content, H 2 O 2 concentration and polymer concentration. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of extraction temperature on characteristics of chicken legskin gelatin

NASA Astrophysics Data System (ADS)

Sompie, M.; Triasih, A.

2018-01-01

Gelatin is a denaturalized protein that is derived from collagen by acidic or alkaline hydrolysis and is an important functional biopolymer that has a very broad application in many industrial fields. Its functional properties depend on processing conditions as well as the raw material. The objective of the research was to study effect of extraction temperature on characteristics of native chicken legskin gelatin. This study used Completely Randomized Design (CRD) with four treatments (T1 = 500C, T2 = 550C, T3 = 600C, T4 = 650C) and five replications. Statistical analysis were carried out by one Anova and the mean difference was tested using Duncan’s Multiple Range Test. The result of research indicated that, extraction temperature had significant effect (P<0.05) on yield, gel strength, viscocity and protein content of chicken legskin gelatin, but it had no significant effect (P>0.05) on water content. It was concluded that the use of extraction temperature 600C was (yields 13.75, gel strength 78.75 g bloom, viscosity 6.52 cP, protein content 84.23% and water content 6.20%).

Investigating the microstructure of keratin extracted from wool: peptide sequence (MALDI-TOF/TOF) and protein conformation (FTIR)

USDA-ARS?s Scientific Manuscript database

Keratin was extracted from wool by reduction with 2-mercaptoethanol. It was isolated as intact keratin and characterized by its similar molecular weight, protein composition, and secondary structure to native keratin. Gel electrophoresis patterns and MALDI-TOF/TOF peptide sequences provided the ide...

Insight into the biochemical, kinetic and spectroscopic characterization of garlic (Allium sativum) phytocystatin: Implication for cardiovascular disease.

PubMed

Siddiqui, Mohd Faizan; Ahmed, Azaj; Bano, Bilqees

2017-02-01

Phytocystatins are cysteine proteinase inhibitors present in plants. They play crucial role in maintaining protease-anti protease balance and are involved in various endogenous processes. Thus, they are suitable and convenient targets for genetic engineering which makes their isolation and characterisation from different sources the need of the hour. In the present study a phytocystatin has been isolated from garlic (Allium sativum) by a simple two-step process using ammonium sulphate fractionation and gel filtration chromatography on Sephacryl S-100HR with a fold purification of 152.6 and yield 48.9%. A single band on native gel electrophoresis confirms the homogeneity of the purified inhibitor. The molecular weight of the purified inhibitor was found to be 12.5kDa as determined by SDS-PAGE and gel filtration chromatography. The garlic phytocystatin was found to be stable under broad range of pH (6-8) and temperature (30°C-60°C). Kinetic studies suggests that garlic phytocystatins are reversible and non-competitive inhibitors having highest affinity for papain followed by ficin and bromelain. UV and fluorescence spectroscopy revealed significant conformational change upon garlic phytocystatin-papain complex formation. Secondary structure analysis was performed using CD and FTIR. Garlic phytocystatin possesses 33.9% alpha-helical content as assessed by CD spectroscopy. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of antimicrobial peptide purification via free-flow electrophoresis and gel filtration chromatography.

PubMed

Xia, Zhi-Jun; Liu, Zhen; Kong, Fan-Zhi; Fan, Liu-Yin; Xiao, Hua; Cao, Cheng-Xi

2017-12-01

Antimicrobial peptides (AMPs) are usually small and cationic biomolecules with broad-spectrum antimicrobial activities against pathogens. Purifying them from complex samples is essential to study their physiochemical properties. In this work, free-flow zone electrophoresis (FFZE) was utilized to purify AMPs from yeast fermentation broth. Meanwhile, gel filtration chromatography (GFC) was conducted for comparison. The separation efficiency was evaluated by SDS-PAGE analysis of the fractions from both methods. Our results demonstrated as follows: (i) FFZE had more than 30-fold higher processing capacity as compared with GFC; (ii) FFZE could achieve 87% purity and 89% recovery rate while in GFC these parameters were about 93 and 82%, respectively; (iii) the former had ∼2-fold dilution but the latter had ∼13-fold dilution. Furthermore, Tricine-SDS-PAGE, Native-PAGE, and gel IEF were carried out to characterize the purified AMPs. We found that two peptides existed as a pair with the molecular mass of ∼5.5 and 7.0 kDa, while the same pI 7.8. These two peptides were proved to have the antimicrobial activity through the standardized agar diffusion method. Therefore, FFZE could be used to continuously purify AMPs with high bioactivity, which will lead to its wide application in the clinical and pharmaceutical fields. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

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

2005-09-30

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

Ribulose-1,5-bis-phosphate carboxylase/oxygenase accumulation factor1 is required for holoenzyme assembly in maize.

PubMed

Feiz, Leila; Williams-Carrier, Rosalind; Wostrikoff, Katia; Belcher, Susan; Barkan, Alice; Stern, David B

2012-08-01

Most life is ultimately sustained by photosynthesis and its rate-limiting carbon fixing enzyme, ribulose-1,5-bis-phosphate carboxylase/oxygenase (Rubisco). Although the structurally comparable cyanobacterial Rubisco is amenable to in vitro assembly, the higher plant enzyme has been refractory to such manipulation due to poor understanding of its assembly pathway. Here, we report the identification of a chloroplast protein required for Rubisco accumulation in maize (Zea mays), RUBISCO ACCUMULATION FACTOR1 (RAF1), which lacks any characterized functional domains. Maize lines lacking RAF1 due to Mutator transposon insertions are Rubisco deficient and seedling lethal. Analysis of transcripts and proteins showed that Rubisco large subunit synthesis in raf1 plants is not compromised; however, newly synthesized Rubisco large subunit appears in a high molecular weight form whose accumulation requires a specific chaperonin 60 isoform. Gel filtration analysis and blue native gels showed that endogenous and recombinant RAF1 are trimeric; however, following in vivo cross-linking, RAF1 copurifies with Rubisco large subunit, suggesting that they interact weakly or transiently. RAF1 is predominantly expressed in bundle sheath chloroplasts, consistent with a Rubisco accumulation function. Our results support the hypothesis that RAF1 acts during Rubisco assembly by releasing and/or sequestering the large subunit from chaperonins early in the assembly process.

Studies on the "Aerobic" Acetyl-Coenzyme A Synthetase of Saccharomyces Cerevisiae: Purification, Crystallization, and Physical Properties of the Enzyme

NASA Technical Reports Server (NTRS)

Satyanarayana, T.; Klein, Harold P.

1976-01-01

A procedure for the purification of a stable acetyl-coenzyme A synthetase (ACS) from aerobic cells of Saccharomyces cerevisiae is presented. The steps include differential centrifugation, solubilization of the bound enzyme from the crude mitochondrial fraction, ammonium sulfate fractionation, crystallization to constant specific activity from ammonium sulfate solutions followed by Bio-Gel A-1.5 m column chromatography. The resulting enzyme preparation is homogeneous as judged by chromatography on Bio-Gel columns, QAE-Sephadex A-50 anion exchange columns, analytical ultracentrifugal studies, and polyacrylamide gel electrophoresis. Sedimentation velocity runs revealed a single symmetric peak with an s(sub (20,w)) value of 10.6. The molecular weight of the native enzyme, as determined by gel filtration and analytical ultracentrifugation, is 250,000 +/- 500. In polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, the molecular weight of the single polypeptide chain is 83,000 +/- 500. The purified enzyme is inhibited by palmityl-coenzyme A with a Hill interaction coefficient, n, of 2.88. These studies indicate that the ACS of aerobic Saccharomyces cerevisiae is composed of three subunits of identical or nearly identical size.

Two dimensional Blue Native-/SDS-PAGE analysis of SLP family adaptor protein complexes.

PubMed

Swamy, Mahima; Kulathu, Yogesh; Ernst, Sandra; Reth, Michael; Schamel, Wolfgang W A

2006-04-15

SH2 domain containing leukocyte protein (SLP) adaptor proteins serve a central role in the antigen-mediated activation of lymphocytes by organizing multiprotein signaling complexes. Here, we use two dimensional native-/SDS-gel electrophoresis to study the number, size and relative abundance of protein complexes containing SLP family proteins. In non-stimulated T cells all SLP-76 proteins are in a approximately 400 kDa complex with the small adaptor protein Grb2-like adaptor protein downstream of Shc (Gads), whereas half of Gads is monomeric. This constitutive SLP-76/Gads complex could be reconstituted in Drosophila S2 cells expressing both components, suggesting that it might not contain additional subunits. In contrast, in B cells SLP-65 exists in a 180 kDa complex as well as in monomeric form. Since the complex was not found in S2 cells expressing only SLP-65, it was not di/trimeric SLP-65. Upon antigen-stimulation only the complexed SLP-65 was phosphorylated. Surprisingly, stimulation-induced alteration of SLP complexes could not be detected, suggesting that active signaling complexes form only transiently, and are of low abundance.

ICPMS analysis of proteins separated by Native-PAGE: Evaluation of metaloprotein profiles in human synovial fluid with acute and chronic arthritis.

PubMed

Moyano, Mario F; Mariño-Repizo, Leonardo; Tamashiro, Héctor; Villegas, Liliana; Acosta, Mariano; Gil, Raúl A

2016-07-01

The role of trace elements bound to proteins in the etiology and pathogenesis of rheumatoid arthritis (RA) remains unclear. In this sense, the identification and detection of metalloproteins has a strong and growing interest. Metalloprotein studies are currently carried out by polyacrylamide gel electrophoresis (PAGE) associated to inductively coupled plasma mass spectrometry (ICPMS), and despite that complete information can be obtained for metals such as Fe, Cu and Zn, difficulties due to poor sensitivity for other trace elements such as Sn, As, etc, are currently faced. In the present work, a simple and fast method for the determination of trace metals bound to synovial fluid (SF) proteins was optimized. Proteins from SF (long and short-term RA) were separated in ten fractions by native PAGE, then dissolved in nitric acid and peroxide hydrogen, and analyzed by ICPMS. Fifteen metals were determined in each separated protein fraction (band). Adequate calibration of proteins molecular weight allowed stablishing which protein type were bound to different metals. Copyright © 2016 Elsevier GmbH. All rights reserved.

Taka-amylase A in the conidia of Aspergillus oryzae RIB40.

PubMed

Nguyen, Cong Ha; Tsurumizu, Ryoji; Sato, Tsutomu; Takeuchi, Michio

2005-11-01

A study of Taka-amylase A of conidia from Aspergillus oryzae RIB40 was done. During the research, proteins from conidia and germinated conidia were analyzed using SDS-PAGE, 2-D gel electrophoresis, Western blot analysis, MALDI-TOF Mass spectrometry, and native-PAGE combined with activity staining of TAA. The results showed that TAA exists not only in germinated conidia but also in conidia. Some bands representing degraded products of TAA were detected. Conidia, which formed on starch (SCYA), glucose (DCYA), and glycerol (GCYA) plates, contained mature TAA. Only one active band of TAA was detected after native-PAGE activity staining. In addition, TAA activity was detected in cell extracts of conidia using 0.5 M acetate buffer, pH 5.2, as extraction buffer, but was not detected in whole conidia or cell debris. The results indicate that TAA exists in conidia in active form even when starch, glucose, or glycerol is used as carbon source. TAA might belong to a set of basal proteins inside conidia, which helps in imbibition and germination of conidia.

Purification and properties of agmatine ureohydrolyase, a putrescine biosynthetic enzyme in Escherichia coli.

PubMed Central

Satishchandran, C; Boyle, S M

1986-01-01

The putrescine biosynthetic enzyme agmatine ureohydrolase (AUH) (EC 3.5.3.11) catalyzes the conversion of agmatine to putrescine in Escherichia coli. AUH was purified approximately 1,600-fold from an E. coli strain transformed with the plasmid pKA5 bearing the speB gene encoding the enzyme. The purification procedure included ammonium sulfate precipitation, heat treatment, and DEAE-sephacel column chromatography. The molecular mass of nondenatured AUH is approximately 80,000 daltons as determined by gel-sieving column chromatography, while on denaturing polyacrylamide gels, the molecular mass is approximately 38,000 daltons; thus, native AUH is most likely a dimer. A radiolabeled protein extracted from minicells carrying the pKA5 plasmid comigrated with the purified AUH in both sodium dodecyl sulfate-polyacrylamide and native polyacrylamide gels. The pI of purified AUH is between 8.2 and 8.4, as determined by either chromatofocusing or isoelectric focusing. The Km of purified AUH for agmatine is 1.2 mM; the pH optimum is 7.3. Neither the numerous ions and nucleotides tested nor polyamines affected AUH activity in vitro. EDTA and EGTA [ethylene glycol-bis (beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid] at 1 mM inactivated AUH activity by 53 and 74%, respectively; none of numerous divalent cations tested restored AUH activity. Ornithine inhibited AUH activity noncompetitively (Ki = 6 X 10(-3) M), while arginine inhibited AUH activity competitively (Ki = 9 X 10(-3) M). Images PMID:3081491

Chemical Synthesis of Sulfated Yeast (Saccharomyces cerevisiae) Glucans and Their In Vivo Antioxidant Activity.

PubMed

Zhang, Hua; Zhang, Jing; Fan, Ziluan; Zhou, Xintao; Geng, Lin; Wang, Zhenyu; Regenstein, Joe M; Xia, Zhiqiang

2017-07-28

The effects of sulfation of yeast glucans was optimized using response surface methodology. The degree of sulfation was evaluated from 0.11 to 0.75 using ion-chromatography. The structural characteristics of SYG (sulfation of yeast glucans) with a DS = 0.75 were determined using high-performance liquid chromatography/gel-permeation chromatography and finally by Fourier transform infrared spectrometry. The SYG had lower viscosity and greater solubility than the native yeast glucans, suggesting that the conformation of the SYG had significantly changed. The results also showed that SYG had a significantly greater antioxidant activity in vivo compared to native yeast glucans.

Toward single cell traction microscopy within 3D collagen matrices

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

Hall, Matthew S.; Long, Rong; Feng, Xinzeng

Mechanical interaction between the cell and its extracellular matrix (ECM) regulates cellular behaviors, including proliferation, differentiation, adhesion, and migration. Cells require the three-dimensional (3D) architectural support of the ECM to perform physiologically realistic functions. However, current understanding of cell–ECM and cell–cell mechanical interactions is largely derived from 2D cell traction force microscopy, in which cells are cultured on a flat substrate. 3D cell traction microscopy is emerging for mapping traction fields of single animal cells embedded in either synthetic or natively derived fibrous gels. We discuss here the development of 3D cell traction microscopy, its current limitations, and perspectives onmore » the future of this technology. Emphasis is placed on strategies for applying 3D cell traction microscopy to individual tumor cell migration within collagen gels. - Highlights: • Review of the current state of the art in 3D cell traction force microscopy. • Bulk and micro-characterization of remodelable fibrous collagen gels. • Strategies for performing 3D cell traction microscopy within collagen gels.« less

Community Analysis and Recovery of Phenol-degrading Bacteria from Drinking Water Biofilters

PubMed Central

Gu, Qihui; Wu, Qingping; Zhang, Jumei; Guo, Weipeng; Wu, Huiqing; Sun, Ming

2016-01-01

Phenol is a ubiquitous organic contaminant in drinking water. Biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. Herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/L phenol within 3 days. PCR detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative attack by phenol hydroxylase, and subsequent ring fission by catechol 1,2-dioxygenase. Based on the PCR denatured gradient gel electrophoresis (PCR-DGGE) profiles of bacteria from biological activated carbon (BAC), the predominant bacteria in drinking water biofilters including Delftia sp., Achromobacter sp., and Agrobacterium sp., which together comprised up to 50% of the total microorganisms. In addition, a shift in bacterial community structure was observed during phenol biodegradation. Furthermore, the most effective phenol-degrading strain DW-1 that correspond to the main band in denaturing gradient gel electrophoresis (DGGE) profile was isolated and identified as Acinetobacter sp., according to phylogenetic analyses of the 16S ribosomal ribonucleic acid (rRNA) gene sequences. The strain DW-1 also produced the most important enzyme, phenol hydroxylase, and it also exhibited a good ability to degrade phenol when immobilized on granular active carbon (GAC). This study indicates that the enrichment culture has great potential application for treatment of phenol-polluted drinking water sources, and the indigenous phenol-degrading microorganism could recover from drinking water biofilters as an efficient resource for phenol removal. Therefore, the aim of this study is to draw attention to recover native phenol-degrading bacteria from drinking water biofilters, and use these native microorganisms as phenolic water remediation in drinking water sources. PMID:27148185

Oligomeric state of purified transient receptor potential melastatin-1 (TRPM1), a protein essential for dim light vision.

PubMed

Agosto, Melina A; Zhang, Zhixian; He, Feng; Anastassov, Ivan A; Wright, Sara J; McGehee, Jennifer; Wensel, Theodore G

2014-09-26

Transient receptor potential melastatin-1 (TRPM1) is essential for the light-induced depolarization of retinal ON bipolar cells. TRPM1 likely forms a multimeric channel complex, although almost nothing is known about the structure or subunit composition of channels formed by TRPM1 or any of its close relatives. Recombinant TRPM1 was robustly expressed in insect cells, but only a small fraction was localized to the plasma membrane. Similar intracellular localization was observed when TRPM1 was heterologously expressed in mammalian cells. TRPM1 was affinity-purified from Sf9 cells and complexed with amphipol, followed by detergent removal. In blue native gels and size exclusion chromatography, TRPM1 migrated with a mobility consistent with detergent- or amphipol-bound dimers. Cross-linking experiments were also consistent with a dimeric subunit stoichiometry, and cryoelectron microscopy and single particle analysis without symmetry imposition yielded a model with approximate 2-fold symmetrical features. Finally, electron microscopy of TRPM1-antibody complexes revealed a large particle that can accommodate TRPM1 and two antibody molecules. Taken together, these data indicate that purified TRPM1 is mostly dimeric. The three-dimensional structure of TRPM1 dimers is characterized by a small putative transmembrane domain and a larger domain with a hollow cavity. Blue native gels of solubilized mouse retina indicate that TRPM1 is present in two distinct complexes: one similar in size to the recombinant protein and one much larger. Because dimers are likely not functional ion channels, these results suggest that additional partner subunits participate in forming the transduction channel required for dim light vision and the ON pathway. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Community Analysis and Recovery of Phenol-degrading Bacteria from Drinking Water Biofilters.

PubMed

Gu, Qihui; Wu, Qingping; Zhang, Jumei; Guo, Weipeng; Wu, Huiqing; Sun, Ming

2016-01-01

Phenol is a ubiquitous organic contaminant in drinking water. Biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. Herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/L phenol within 3 days. PCR detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative attack by phenol hydroxylase, and subsequent ring fission by catechol 1,2-dioxygenase. Based on the PCR denatured gradient gel electrophoresis (PCR-DGGE) profiles of bacteria from biological activated carbon (BAC), the predominant bacteria in drinking water biofilters including Delftia sp., Achromobacter sp., and Agrobacterium sp., which together comprised up to 50% of the total microorganisms. In addition, a shift in bacterial community structure was observed during phenol biodegradation. Furthermore, the most effective phenol-degrading strain DW-1 that correspond to the main band in denaturing gradient gel electrophoresis (DGGE) profile was isolated and identified as Acinetobacter sp., according to phylogenetic analyses of the 16S ribosomal ribonucleic acid (rRNA) gene sequences. The strain DW-1 also produced the most important enzyme, phenol hydroxylase, and it also exhibited a good ability to degrade phenol when immobilized on granular active carbon (GAC). This study indicates that the enrichment culture has great potential application for treatment of phenol-polluted drinking water sources, and the indigenous phenol-degrading microorganism could recover from drinking water biofilters as an efficient resource for phenol removal. Therefore, the aim of this study is to draw attention to recover native phenol-degrading bacteria from drinking water biofilters, and use these native microorganisms as phenolic water remediation in drinking water sources.

Development and Characterization of Titanium Dioxide Gel with Encapsulated Bacteriorhodopsin for Hydrogen Production.

PubMed

Johnson, Kaitlin E; Gakhar, Sukriti; Risbud, Subhash H; Longo, Marjorie L

2018-06-06

We study bacteriorhodopsin (BR) in its native purple membrane encapsulated within amorphous titanium dioxide, or titania, gels and in the presence of titania sol-particles to explore this system for hydrogen production. Förster resonance energy transfer between BR and titanium dioxide sol particles was used to conclude that there is nanometer-scale proximity of bacteriorhodopsin to the titanium dioxide. The detection of BR-titania sol aggregates by fluorescence anisotropy and particle sizing indicated the affinity amorphous titania has for BR without the use of additional cross-linkers. UV-Visible spectroscopy of BR-titania gels show that methanol addition did not denature BR at a 25 mM concentration presence as a sacrificial electron donor. Additionally, confinement of BR in the gels significantly limited protein denaturation at higher concentration of added methanol or ethanol. Subsequently, titania gels fabricated through the sol-gel process using a titanium ethoxide precursor, water and the addition of 25 mM methanol were used to encapsulate BR and a platinum reduction catalyst for the production of hydrogen gas under white light irradiation. The inclusion of 5 µM bacteriorhodopsin resulted in a hydrogen production rate of about 3.8 µmole hydrogen mL -1 hr -1 , an increase of 52% compared to gels containing no protein. Electron transfer and proton pumping by BR in close proximity to the titania gel surface are feasible explanations for the enhanced production of hydrogen without the need to crosslink BR to the titania gel. This work sets the stage for further developments of amorphous, rather than crystalline, titania-encapsulated bacteriorhodopsin for solar-driven hydrogen production through water-splitting.

Partial purification and characterization of a Ca(2+)-dependent protein kinase from the green alga, Dunaliella salina

NASA Technical Reports Server (NTRS)

Roux, S. J.

1990-01-01

A calcium-dependent protein kinase was partially purified and characterized from the green alga Dunaliella salina. The enzyme was activated at free Ca2+ concentrations above 10(-7) molar. and half-maximal activation was at about 3 x 10(-7) molar. The optimum pH for its Ca(2+)-dependent activity was 7.5. The addition of various phospholipids and diolein had no effects on enzyme activity and did not alter the sensitivity of the enzyme toward Ca2+. The enzyme was inhibited by calmodulin antagonists, N-(6-aminohexyl)-1-naphthalene sulfonamide and N-(6-aminohexyl)-5-chloro-1-naphthalene sulfonamide in a dose-dependent manner while the protein kinase C inhibitor, sphingosine, had little effect on enzyme activity up to 800 micromolar. Immunoassay showed some calmodulin was present in the kinase preparations. However, it is unlikely the kinase was calmodulin regulated, since it still showed stimulation by Ca2+ in gel assays after being electrophoretically separated from calmodulin by two different methods. This gel method of detection of the enzyme indicated that a protein band with an apparent molecular weight of 40,000 showed protein kinase activity at each one of the several steps in the purification procedure. Gel assay analysis also showed that after native gel isoelectric focusing the partially purified kinase preparations had two bands with calcium-dependent activity, at isoelectric points 6.7 and 7.1. By molecular weight, by isoelectric point, and by a comparative immunoassay, the Dunaliella kinase appears to differ from at least some of the calcium-dependent, but calmodulin and phospholipid independent kinases described from higher plants.

Selective tuning of the self-assembly and gelation of a hydrophilic poloxamine by cyclodextrins.

PubMed

González-Gaitano, Gustavo; da Silva, Marcelo A; Radulescu, Aurel; Dreiss, Cécile A

2015-05-26

Complexes formed between cyclodextrins (CDs) and polymers - pseudopolyrotaxanes (PPRs) - are the starting point of a multitude of supramolecular structures, which are proposed for a wide range of biomedical and technological applications. In this work, we investigate the complexation of a range of cyclodextrins with Tetronic T1307, a four-arm block copolymer of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) with a pH-responsive central ethylene diamine spacer, and its impact on micellization and the sol-gel transition. At low concentrations, small-angle neutron scattering (SANS) combined with dynamic light scattering (DLS) measurements show the presence of spherical micelles with a highly hydrated shell and a dehydrated core. Increasing the temperature leads to more compact micelles and larger aggregation numbers, whereas acidic conditions induce a shrinking of the micelles, with fewer unimers per micelle and a more hydrated corona. At high concentrations, T1307 undergoes a sol-gel transition, which is suppressed at pH below the pKa,1 (4.6). SANS data analysis reveals that the gels result from a random packing of the micelles, which have an increasing aggregation number and increasingly dehydrated shell and hydrated core with the temperature. Native CDs (α, β, γ-CD) can complex T1307, resulting in the precipitation of a PPR. Instead, modified CDs compete with micellization to an extent that is critically dependent on the nature of the substitution. (1)H and ROESY NMR combined with SANS demonstrate that dimethylated β-CD can thread onto the polymer, preferentially binding to the PO units, thus hindering self-aggregation by solubilizing the hydrophobic block. The various CDs are able to modulate the onset of gelation and the extent of the gel phase, and the effect correlates with the ability of the CDs to disrupt the micelles, with the exception of a sulfated sodium salt of β-CD, which, while not affecting the CMT, is able to fully suppress the gel phase.

Use of procainamide gels in the purification of human and horse serum cholinesterases.

PubMed Central

Ralston, J S; Main, A R; Kilpatrick, B F; Chasson, A L

1983-01-01

Two large-scale methods based primarily on the use of procainamide-Sepharose gels were developed for the purification of horse and human serum non-specific cholinesterases. With method I, the procainamide-Sepharose 4B gel was used in the first step to handle large volumes of serum. With method II, the procainamide-Sepharose 4B gel was used in the final step to obtain pure enzyme. Although both methods gave electrophoretically pure cholinesterase preparations in good yields, they were significantly more efficient at purifying the horse enzyme than the human enzyme. To study this problem, the relative binding of human and horse cholinesterases to procainamide-, methylacridinium (MAC)-, m-trimethylammoniophenyl (m-PTA)- and p-trimethylammoniophenyl (p-PTA)-Sepharose 4B gels were measured, by using two approaches. In one, binding was measured by a procedure involving equilibration of pure cholinesterase in a small volume of diluted gel slurry (4%, v/v). A partially purified preparation of Electrophorus acetylcholinesterase was included. Pure human cholinesterase bound consistently more tightly to each of the gels than did horse cholinesterase, and the acetylcholinesterase appeared to bind the gels 10-100 times more tightly than did the non-specific cholinesterases. The order of binding for the cholinesterases, beginning with the tightest, was: procainamide-Sepharose 4B, MAC-Sepharose 4B, p-PTA-Sepharose 4B and m-PTA-Sepharose 4B. For the acetylcholinesterase the order was: MAC-Sepharose 4B, procainamide-Sepharose 4B, p-PTA-Sepharose 4B and m-PTA-Sepharose 4B. The second approach involved passing native sera or partially purified sera fractions through 1 ml test columns of each of the four affinity gels to determine their retention capacity for the cholinesterases. With these impure samples, the MAC-Sepharose 4B gels proved superior to the procainamide-Sepharose 4B gels at retaining human cholinesterase, but the opposite was true for the horse cholinesterase. PMID:6870822

A multi-channel gel electrophoresis and continuous fraction collection apparatus for high throughput protein separation and characterization

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

Choi, Megan; Nordmeyer, Robert A.; Cornell, Earl

2009-10-02

To facilitate a direct interface between protein separation by PAGE and protein identification by mass spectrometry, we developed a multichannel system that continuously collects fractions as protein bands migrate off the bottom of gel electrophoresis columns. The device was constructed using several short linear gel columns, each of a different percent acrylamide, to achieve a separation power similar to that of a long gradient gel. A Counter Free-Flow elution technique then allows continuous and simultaneous fraction collection from multiple channels at low cost. We demonstrate that rapid, high-resolution separation of a complex protein mixture can be achieved on this systemmore » using SDS-PAGE. In a 2.5 h electrophoresis run, for example, each sample was separated and eluted into 48-96 fractions over a mass range of 10-150 kDa; sample recovery rates were 50percent or higher; each channel was loaded with up to 0.3 mg of protein in 0.4 mL; and a purified band was eluted in two to three fractions (200 L/fraction). Similar results were obtained when running native gel electrophoresis, but protein aggregation limited the loading capacity to about 50 g per channel and reduced resolution.« less

Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins

PubMed Central

Dallas, David C.; Citerne, Florine; Tian, Tian; Silva, Vitor L. M.; Kalanetra, Karen M.; Frese, Steven A.; Robinson, Randall C.; Mills, David A.; Barile, Daniela

2015-01-01

Scope The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Methods and results Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1,500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. Conclusion The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. PMID:26616950

Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins.

PubMed

Dallas, David C; Citerne, Florine; Tian, Tian; Silva, Vitor L M; Kalanetra, Karen M; Frese, Steven A; Robinson, Randall C; Mills, David A; Barile, Daniela

2016-04-15

The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Using Electrophoretic Mobility Shift Assays to Measure Equilibrium Dissociation Constants: GAL4-p53 Binding DNA as a Model System

ERIC Educational Resources Information Center

Heffler, Michael A.; Walters, Ryan D.; Kugel, Jennifer F.

2012-01-01

An undergraduate biochemistry laboratory experiment is described that will teach students the practical and theoretical considerations for measuring the equilibrium dissociation constant (K[subscript D]) for a protein/DNA interaction using electrophoretic mobility shift assays (EMSAs). An EMSA monitors the migration of DNA through a native gel;…

Simple, high-yield purification of xanthine oxidase from bovine milk.

PubMed

Ozer, N; Müftüoglu, M; Ataman, D; Ercan, A; Ogüs, I H

1999-05-13

Xanthine oxidase, a commercially important enzyme with a wide area of application, was extracted from fresh milk, without added preservatives, using toluene and heat. The short purification procedure, with high yield, consisted of extraction, ammonium sulfate fractionation, and DEAE-Sepharose (fast flow) column chromatography. Xanthine oxidase was eluted as a single activity peak from the column using a buffer gradient. The purification fold, specific activity and yield for the purified xanthine oxidase were 328, 10.161 U/mg and 69%, respectively. The enzyme was concentrated by ultrafiltration, although 31% of the activity was lost during concentration, no change in specific activity was observed. Activity and protein gave coincident staining bands on native polyacrylamide gels. The intensity and the number of bands were dependent on the oxidative state(s) of the enzyme; reduction by 2-mercaptoethanol decreased the intensity of the slow-moving bands and increased the intensity of the fastest-moving band. Following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), two major bands (molecular masses of 152 and 131 kDa) were observed, accounting for > or = 95% of xanthine oxidase. Native- and SDS-PAGE showed that the purified xanthine oxidase becomes a heterodimer due to endogenous proteases.

A chiral BINOL-based Gemini amphiphilic gelator and its specific discrimination of native arginine by gelation in water.

PubMed

Jia, Lihua; Yin, Jianxin; Guo, Xiangfeng; Cao, Guangzhou; Tian, Xuhua; Zhu, Bo; Pu, Lin

2017-08-16

A novel axially chiral cationic Gemini amphiphile gelator (S1) derived from (S)-BINOL has been synthesized and characterized by 1 H NMR, 13 C NMR, ESI-MS and FT-IR analyses. The critical micelle concentration (CMC) of S1 was determined to be 0.21 mM in water at room temperature. A transparent hydrogel with S1 at 43 mM was obtained at room temperature and characterized using various methods including SEM, CD, fluorescence, 1 H NMR, FT-IR, and XRD. The results indicate that the hydrophobic effect of long alkyl chains, π-π stacking of naphthalene rings, and intermolecular hydrogen-bonding of the amide groups of S1 should be responsible for the hydrogel formation. Moreover, an 8.5 mM aqueous solution of S1 could gel by the addition of l-arginine, whereas it failed to gel in the presence of other 15 amino acids, respectively. It is suggested that S1 could discriminate native arginine by hydrogel formation, mainly due to the electrostatic interaction and hydrogen bonding effects between S1 and l-arginine molecules.

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

Effect of synthesis route on electrical and ethanol sensing characteristics for LaFeO3-δ nanoparticles by citric sol-gel method

NASA Astrophysics Data System (ADS)

Cao, Ensi; Yang, Yuqing; Cui, Tingting; Zhang, Yongjia; Hao, Wentao; Sun, Li; Peng, Hua; Deng, Xiao

2017-01-01

LaFeO3-δ nanoparticles were prepared by citric sol-gel method with different raw material choosing and calcination process. The choosing of polyethylene glycol instead of ethylene glycol as raw material and additional pre-calcination at 400 °C rather than direct calcination at 600 °C could result in the decrease of resistance due to the reduction of activation energy Ea. Meanwhile, the choosing of ethylene glycol as raw material and additional pre-calcination leads to the enhancement of sensitivity to ethanol. Comprehensive analysis on the sensitivity and XRD, SEM, TEM, XPS results indicates that the sensing performance of LaFeO3-δ should be mainly determined by the adsorbed oxygen species on Fe ions, with certain contribution from native active oxygen. The best sensitivity of 46.1-200 ppm ethanol at prime working temperature of 112 °C is obtained by the sample using ethylene glycol as raw material with additional pre-calcination, which originates from its uniformly-sized and well-dispersed particles as well as high atomic ratio of Fe/La at surface region.

Purification and characterization of selenium-containing phycocyanin from selenium-enriched Spirulina platensis.

PubMed

Chen, Tianfeng; Wong, Yum-Shing; Zheng, Wenjie

2006-11-01

A fast protein liquid chromatographic method for purification of selenium-containing phycocyanin (Se-PC) from selenium-enriched Spirulina platensis was described in this study. The purification procedures involved fractionation by ammonium sulfate precipitation, DEAE-Sepharose ion-exchange chromatography and Sephacry S-300 size exclusion chromatography. The purity ratio (A620/A280) and the separation factor (A620/A655) of the purified Se-PC were 5.12 and 7.92, respectively. The Se concentration of purified Se-PC was 496.5 microg g(-1) protein, as determined by ICP-AES analysis. The purity of the Se-PC was further characterized by UV-VIS and fluorescence spectrometry, SDS-PAGE, RP-HPLC and gel filtration HPLC. The apparent molecular mass of the native Se-PC determined by gel filtration HPLC was 109 kDa, indicating that the protein existed as a trimer. SDS-PAGE of the purified Se-PC yielded two major bands corresponding to the alpha and beta subunits. A better separation of these two subunits was obtained by RP-HPLC. Identification of the alpha and beta subunits separated by SDS-PAGE and RP-HPLC was achieved by peptide mass fingerprinting (PMF) using MALDI-TOF-TOF mass spectrometry.

Matrix-associated implantation of predifferentiated mesenchymal stem cells versus articular chondrocytes: in vivo results of cartilage repair after 1 year.

PubMed

Marquass, Bastian; Schulz, Ronny; Hepp, Pierre; Zscharnack, Matthias; Aigner, Thomas; Schmidt, Stefanie; Stein, Frank; Richter, Robert; Osterhoff, Georg; Aust, Gabriele; Josten, Christoph; Bader, Augustinus

2011-07-01

The use of predifferentiated mesenchymal stem cells (MSC) leads to better histological results compared with undifferentiated MSC in sheep. This raises the need for a longer term follow-up study and comparison with a clinically established method. We hypothesized that chondrogenic in vitro predifferentiation of autologous MSC embedded in a collagen I hydrogel leads to better structural repair of a chronic osteochondral defect in an ovine stifle joint after 1 year. We further hypothesized that resulting histological results would be comparable with those of chondrocyte-seeded matrix-associated autologous chondrocyte transplantation (MACT). Controlled laboratory study. Predifferentiation period of ovine MSC within collagen gel in vitro was defined by assessment of several cellular and molecular biological parameters. For the animal study, 2 osteochondral lesions (7-mm diameter) were created at the medial femoral condyles of the hind legs in 9 sheep. Implantation of MSC gels was performed 6 weeks after defect creation. Thirty-six defects were divided into 4 treatment groups: (1) chondrogenically predifferentiated MSC gels (pre-MSC gels), (2) undifferentiated MSC gels (un-MSC gels), (3) MACT gels, and (4) untreated controls (UC). Histological, immunohistochemical, and radiological evaluations followed after 12 months. After 12 months in vivo, pre-MSC gels showed significantly better histological outcome compared with un-MSC gels and UC. Compared with MACT gels, the overall scores were higher for O'Driscoll and International Cartilage Repair Society (ICRS). The repair tissue of the pre-MSC group showed immunohistochemical detection of interzonal collagen type II staining. Radiological evaluation supported superior bonding of pre-MSC gels to perilesional native cartilage. Compared with previous work by our group, no degradation of the repair tissue between 6 and 12 months in vivo, particularly in pre-MSC gels, was observed. Repair of chronic osteochondral defects with collagen hydrogels composed of chondrogenically predifferentiated MSC shows no signs of degradation after 1 year in vivo. In addition, pre-MSC gels lead to partially superior histological results compared with articular chondrocytes. The results suggest an encouraging method for future treatment of focal osteochondral defects without donor site morbidity by harvesting articular chondrocytes.

Ribulose-1,5-Bis-Phosphate Carboxylase/Oxygenase Accumulation Factor1 Is Required for Holoenzyme Assembly in Maize[C][W

PubMed Central

Feiz, Leila; Williams-Carrier, Rosalind; Wostrikoff, Katia; Belcher, Susan; Barkan, Alice; Stern, David B.

2012-01-01

Most life is ultimately sustained by photosynthesis and its rate-limiting carbon fixing enzyme, ribulose-1,5-bis-phosphate carboxylase/oxygenase (Rubisco). Although the structurally comparable cyanobacterial Rubisco is amenable to in vitro assembly, the higher plant enzyme has been refractory to such manipulation due to poor understanding of its assembly pathway. Here, we report the identification of a chloroplast protein required for Rubisco accumulation in maize (Zea mays), RUBISCO ACCUMULATION FACTOR1 (RAF1), which lacks any characterized functional domains. Maize lines lacking RAF1 due to Mutator transposon insertions are Rubisco deficient and seedling lethal. Analysis of transcripts and proteins showed that Rubisco large subunit synthesis in raf1 plants is not compromised; however, newly synthesized Rubisco large subunit appears in a high molecular weight form whose accumulation requires a specific chaperonin 60 isoform. Gel filtration analysis and blue native gels showed that endogenous and recombinant RAF1 are trimeric; however, following in vivo cross-linking, RAF1 copurifies with Rubisco large subunit, suggesting that they interact weakly or transiently. RAF1 is predominantly expressed in bundle sheath chloroplasts, consistent with a Rubisco accumulation function. Our results support the hypothesis that RAF1 acts during Rubisco assembly by releasing and/or sequestering the large subunit from chaperonins early in the assembly process. PMID:22942379

Analysis of the Aspergillus fumigatus proteome reveals metabolic changes and the activation of the pseurotin A biosynthesis gene cluster in response to hypoxia.

PubMed

Vödisch, Martin; Scherlach, Kirstin; Winkler, Robert; Hertweck, Christian; Braun, Hans-Peter; Roth, Martin; Haas, Hubertus; Werner, Ernst R; Brakhage, Axel A; Kniemeyer, Olaf

2011-05-06

The mold Aspergillus fumigatus is the most important airborne fungal pathogen. Adaptation to hypoxia represents an important virulence attribute for A. fumigatus. Therefore, we aimed at obtaining a comprehensive overview about this process on the proteome level. To ensure highly reproducible growth conditions, an oxygen-controlled, glucose-limited chemostat cultivation was established. Two-dimensional gel electrophoresis analysis of mycelial and mitochondrial proteins as well as two-dimensional Blue Native/SDS-gel separation of mitochondrial membrane proteins led to the identification of 117 proteins with an altered abundance under hypoxic in comparison to normoxic conditions. Hypoxia induced an increased activity of glycolysis, the TCA-cycle, respiration, and amino acid metabolism. Consistently, the cellular contents in heme, iron, copper, and zinc increased. Furthermore, hypoxia induced biosynthesis of the secondary metabolite pseurotin A as demonstrated at proteomic, transcriptional, and metabolite levels. The observed and so far not reported stimulation of the biosynthesis of a secondary metabolite by oxygen depletion may also affect the survival of A. fumigatus in hypoxic niches of the human host. Among the proteins so far not implicated in hypoxia adaptation, an NO-detoxifying flavohemoprotein was one of the most highly up-regulated proteins which indicates a link between hypoxia and the generation of nitrosative stress in A. fumigatus.

Identification of differentially accumulated proteins associated with embryogenic and non-embryogenic calli in saffron (Crocus sativus L.)

PubMed Central

2012-01-01

Background Somatic embryogenesis (SE) is a complex biological process that occurs under inductive conditions and causes fully differentiated cells to be reprogrammed to an embryo like state. In order to get a better insight about molecular basis of the SE in Crocus sativus L. and to characterize differentially accumulated proteins during the process, a proteomic study based on two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry has been carried out. Results We have compared proteome profiles of non-embryogenic and embryogenic calli with native corm explants. Total soluble proteins were phenol-extracted and loaded on 18 cm IPG strips for the first dimension and 11.5% sodium dodecyl sulfate-polyacrylamide gels for the second dimension. Fifty spots with more than 1.5-fold change in abundance were subjected to mass spectrometry analysis for further characterization. Among them 36 proteins could be identified, which are classified into defense and stress response, protein synthesis and processing, carbohydrate and energy metabolism, secondary metabolism, and nitrogen metabolism. Conclusion Our results showed that diverse cellular and molecular processes were affected during somatic to embryogenic transition. Differential proteomic analysis suggests a key role for ascorbate metabolism during early stage of SE, and points to the possible role of ascorbate-glutathione cycle in establishing somatic embryos. PMID:22243837

Successful transplantation of in vitro expanded human cadaver corneal endothelial precursor cells on to a cadaver bovine's eye using a nanocomposite gel sheet.

PubMed

Parikumar, Periyasamy; Haraguchi, Kazutoshi; Ohbayashi, Akira; Senthilkumar, Rajappa; Abraham, Samuel J K

2014-05-01

In vitro expansion of human corneal endothelial precursor (HCEP) cells has been reported via production of cell aggregated spheres. However, to translate this procedure in human patients warrants maintaining the position of the eyeballs facing down for 36 h, which is not feasible. In this study, we report a method using a nanocomposite (NC) gel sheet to accomplish the integration of HCEP cells to the endothelium of cadaver bovine's eyes. HCEP cells were isolated from the corneal endothelium of a cadaver human eye and then expanded using a thermoreversible gelation polymer (TGP) as reported earlier. For the study, three cadaver bovine eyes were used. The NC gel sheets were inserted into the bovine eyes', aligned and suture-fixed in position under the host endothelium. HCEP cells previously expanded in the TGP were harvested and injected using a 26-gauge syringe between the endothelium and the NC gel sheet. The eyes were left undisturbed for three hours following which the NC gel sheets were gently removed. The corneas were harvested and subjected to histopathological studies. Histopathological studies showed that all the three corneas used for NC gel sheet implantation showed the presence of engrafted HCEP cells, seen as multi-layered cells over the native endothelium of the bovine cornea. Examination of the NC gel sheets used for implantation showed that only very few corneal endothelial cells remained on the sheets amounting to what could be considered negligible. The use of the NC gel sheet makes HCEP cell transplantation feasible for human patients. Further in vitro basic studies followed by translational studies are necessary to bring this method for clinical application in appropriate indications.

Articular cartilage generation applying PEG-LA-DM/PEGDM copolymer hydrogels.

PubMed

Zhao, Xing; Papadopoulos, Anestis; Ibusuki, Shinichi; Bichara, David A; Saris, Daniel B; Malda, Jos; Anseth, Kristi S; Gill, Thomas J; Randolph, Mark A

2016-06-03

Injuries to the human native cartilage tissue are particularly problematic because cartilage has little to no ability to heal or regenerate itself. Employing a tissue engineering strategy that combines suitable cell sources and biomimetic hydrogels could be a promising alternative to achieve cartilage regeneration. However, the weak mechanical properties may be the major drawback to use fully degradable hydrogels. Besides, most of the fully degradable hydrogels degrade too fast to permit enough extracellular matrix (ECM) production for neocartilage formation. In this study, we demonstrated the feasibility of neocartilage regeneration using swine articular chondrocytes photoencapsualted into poly (ethylene glycol) dimethacrylate (PEGDM) copolymer hydrogels composed of different degradation profiles: degradable (PEG-LA-DM) and nondegradable (PEGDM) macromers in molar ratios of 50/50, 60/40, 70/30, 80/20, and 90/10. Articular chondrocytes were isolated enzymatically from juvenile Yorkshire swine cartilage. 6 × 10(7) cells cells were added to each milliliter of macromer/photoinitiator (I2959) solution. Nonpolymerized gel containing the cells (100 μL) was placed in cylindrical molds (4.5 mm diameter × 6.5 mm in height). The macromer/photoinitiator/chondrocyte solutions were polymerized using ultraviolet (365 nm) light at 10 mW/cm(2) for 10 mins. Also, an articular cartilaginous ring model was used to examine the capacity of the engineered cartilage to integrate with native cartilage. Samples in the pilot study were collected at 6 weeks. Samples in the long-term experimental groups (60/40 and 70/30) were implanted into nude mice subcutaneously and harvested at 6, 12 and 18 weeks. Additionally, cylindrical constructs that were not implanted used as time zero controls. All of the harvested specimens were examined grossly and analyzed histologically and biochemically. Histologically, the neocartilage formed in the photochemically crosslinked gels resembled native articular cartilage with chondrocytes in lacunae and surrounded by new ECM. Increases in total DNA, glycosaminoglycan, and hydroxyproline were observed over the time periods studied. The neocartilage integrated with existing native cartilage. Articular cartilage generation was achieved using swine articular chondrocytes photoencapsulated in copolymer PEGDM hydrogels, and the neocartilage tissue had the ability to integrate with existing adjacent native cartilage.

Two-dimensional blue native/SDS-PAGE analysis of whole cell lysate protein complexes of rice in response to salt stress.

PubMed

Hashemi, Amenehsadat; Gharechahi, Javad; Nematzadeh, Ghorbanali; Shekari, Faezeh; Hosseini, Seyed Abdollah; Salekdeh, Ghasem Hosseini

2016-08-01

To understand the biology of a plant in response to stress, insight into protein-protein interactions, which almost define cell behavior, is thought to be crucial. Here, we provide a comparative complexomics analysis of leaf whole cell lysate of two rice genotypes with contrasting responses to salt using two-dimensional blue native/SDS-PAGE (2D-BN/SDS-PAGE). We aimed to identify changes in subunit composition and stoichiometry of protein complexes elicited by salt. Using mild detergent for protein complex solubilization, we were able to identify 9 protein assemblies as hetero-oligomeric and 30 as homo-oligomeric complexes. A total of 20 proteins were identified as monomers in the 2D-BN/SDS-PAGE gels. In addition to identifying known protein complexes that confirm the technical validity of our analysis, we were also able to discover novel protein-protein interactions. Interestingly, an interaction was detected for glycolytic enzymes enolase (ENO1) and triosephosphate isomerase (TPI) and also for a chlorophyll a-b binding protein and RuBisCo small subunit. To show changes in subunit composition and stoichiometry of protein assemblies during salt stress, the differential abundance of interacting proteins was compared between salt-treated and control plants. A detailed exploration of some of the protein complexes provided novel insight into the function, composition, stoichiometry and dynamics of known and previously uncharacterized protein complexes in response to salt stress. Copyright © 2016 Elsevier GmbH. All rights reserved.

Sea Spray Aerosol Structure and Composition Using Cryogenic Transmission Electron Microscopy

PubMed Central

2016-01-01

The composition and surface properties of atmospheric aerosol particles largely control their impact on climate by affecting their ability to uptake water, react heterogeneously, and nucleate ice in clouds. However, in the vacuum of a conventional electron microscope, the native surface and internal structure often undergo physicochemical rearrangement resulting in surfaces that are quite different from their atmospheric configurations. Herein, we report the development of cryogenic transmission electron microscopy where laboratory generated sea spray aerosol particles are flash frozen in their native state with iterative and controlled thermal and/or pressure exposures and then probed by electron microscopy. This unique approach allows for the detection of not only mixed salts, but also soft materials including whole hydrated bacteria, diatoms, virus particles, marine vesicles, as well as gel networks within hydrated salt droplets—all of which will have distinct biological, chemical, and physical processes. We anticipate this method will open up a new avenue of analysis for aerosol particles, not only for ocean-derived aerosols, but for those produced from other sources where there is interest in the transfer of organic or biological species from the biosphere to the atmosphere. PMID:26878061

Proteomic analysis reveals contrasting stress response to uranium in two nitrogen-fixing Anabaena strains, differentially tolerant to uranium.

PubMed

Panda, Bandita; Basu, Bhakti; Acharya, Celin; Rajaram, Hema; Apte, Shree Kumar

2017-01-01

Two strains of the nitrogen-fixing cyanobacterium Anabaena, native to Indian paddy fields, displayed differential sensitivity to exposure to uranyl carbonate at neutral pH. Anabaena sp. strain PCC 7120 and Anabaena sp. strain L-31 displayed 50% reduction in survival (LD 50 dose), following 3h exposure to 75μM and 200μM uranyl carbonate, respectively. Uranium responsive proteome alterations were visualized by 2D gel electrophoresis, followed by protein identification by MALDI-ToF mass spectrometry. The two strains displayed significant differences in levels of proteins associated with photosynthesis, carbon metabolism, and oxidative stress alleviation, commensurate with their uranium tolerance. Higher uranium tolerance of Anabaena sp. strain L-31 could be attributed to sustained photosynthesis and carbon metabolism and superior oxidative stress defense, as compared to the uranium sensitive Anabaena sp. strain PCC 7120. Uranium responsive proteome modulations in two nitrogen-fixing strains of Anabaena, native to Indian paddy fields, revealed that rapid adaptation to better oxidative stress management, and maintenance of metabolic and energy homeostasis underlies superior uranium tolerance of Anabaena sp. strain L-31 compared to Anabaena sp. strain PCC 7120. Copyright © 2016 Elsevier B.V. All rights reserved.

Purification and properties of a beta-1,3-glucanase from Chaetomium sp. that is involved in mycoparasitism.

PubMed

Sun, Hui; Yang, Jinkui; Lin, Chao; Huang, Xiaowei; Xing, Ruihuan; Zhang, Ke-Qin

2006-01-01

A beta-1,3-glucanase was detected, using laminarin as substrate, in the culture broth of Chaetomium sp. Major activity was associated with a 70 kDa protein band visualized on a polyacrylamide gel. beta-1,3-Glucanase was purified by a one-step, native gel purification procedure. Optimal activity was observed at pH 6.0 and 30 degrees C (over 30 min). It could degrade cell walls of plant pathogens including Rhizoctonia solani, Gibberella zeae, Fusarium sp., Colletotrichum gloeosporioides and Phoma sp. The N-terminal amino acid residues of the purified beta-1,3-glucanase are PYQLQTP, which do not exhibit homology to other fungal beta-1,3-glucanases suggesting it may be a novel enzyme.

Stability of spermine oxidase to thermal and chemical denaturation: comparison with bovine serum amine oxidase.

PubMed

Cervelli, Manuela; Leonetti, Alessia; Cervoni, Laura; Ohkubo, Shinji; Xhani, Marla; Stano, Pasquale; Federico, Rodolfo; Polticelli, Fabio; Mariottini, Paolo; Agostinelli, Enzo

2016-10-01

Spermine oxidase (SMOX) is a flavin-containing enzyme that specifically oxidizes spermine to produce spermidine, 3-aminopropanaldehyde and hydrogen peroxide. While no crystal structure is available for any mammalian SMOX, X-ray crystallography showed that the yeast Fms1 polyamine oxidase has a dimeric structure. Based on this scenario, we have investigated the quaternary structure of the SMOX protein by native gel electrophoresis, which revealed a composite gel band pattern, suggesting the formation of protein complexes. All high-order protein complexes are sensitive to reducing conditions, showing that disulfide bonds were responsible for protein complexes formation. The major gel band other than the SMOX monomer is the covalent SMOX homodimer, which was disassembled by increasing the reducing conditions, while being resistant to other denaturing conditions. Homodimeric and monomeric SMOXs are catalytically active, as revealed after gel staining for enzymatic activity. An engineered SMOX mutant deprived of all but two cysteine residues was prepared and characterized experimentally, resulting in a monomeric species. High-sensitivity differential scanning calorimetry of SMOX was compared with that of bovine serum amine oxidase, to analyse their thermal stability. Furthermore, enzymatic activity assays and fluorescence spectroscopy were used to gain insight into the unfolding process.

Utilization of modified starch from avocado (Persea americana Mill.) seed in cream soup production

NASA Astrophysics Data System (ADS)

Cornelia, M.; Christianti, A.

2018-01-01

Avocado (Persea americana Mill.) seed was often seen as waste and underutilized resources, especially in the food industry. The aim of this research was to modify the structure of avocado seed starch using the cross-linking method, to improve the viscosity stability in the cream soup. In the preliminary research, starch was isolated from the seed and modified by STPP (sodium tripolyphosphate) with 2%, 4%, and 6% concentration and were reacted for 1, 2, and 3 hours. Starches were analyzed for moisture and ash content, paste clarity, gel strength, swelling power, solubility, yield, and degree of whiteness. Based on the analysis results, the best reaction time and STPP concentration was 6% at 1 hour reaction time. Native starch and the best-modified starch were applied in the cream soup and compared with commercial cream soup. Cream soups were analyzed for viscosity stability using viscometer in 0, 1, 3, and 5 hours after storage in room temperature. The result showed that cream soup using modified starch has better viscosity stability than native starch and commercial cream soup after 5 hours storage, which was 181.7 ± 4.85 cP. Sensory analysis showed that cream soup using modified starch was more acceptable than the others. Avocado seed modified starch has phosphate group that strengthen the starch chain to prevent viscosity breakdown.

Biochemical characterization of Aspergillus oryzae native tannase and the recombinant enzyme expressed in Pichia pastoris.

PubMed

Mizuno, Toshiyuki; Shiono, Yoshihito; Koseki, Takuya

2014-10-01

In this study, the biochemical properties of the recombinant tannase from Aspegillus oryzae were compared with those of the native enzyme. Extracellular native tannase was purified from a commercial enzyme source. Recombinant tannase highly expressed in Pichia pastoris was prepared as an active extracellular protein. Purified native and recombinant tannases produced smeared bands with apparent molecular masses of 45-80 kDa and 45-75 kDa, respectively, by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. After N-deglycosylation, the native enzyme yielded molecular masses of 33 kDa and 30 kDa, whereas the recombinant enzyme yielded molecular masses of 34 kDa and 30 kDa. Purified native and recombinant tannases had an optimum pH of 4.0-5.0 and 5.0, respectively, and were stable up to 40°C. After N-deglycosylation, both enzymes exhibited reduced thermostability. Catalytic efficiencies of both purified enzymes were greater with natural substrates, such as (-)-catechin, (-)-epicatechin, and (-)-epigallocatechin gallates, than those with synthetic substrates, such as methyl, ethyl, and propyl gallates. However, there were no activities against the methyl esters of ferulic, p-coumaric, caffeic, and sinapic acids, which indicate feruloyl esterase activity, or the ethyl, propyl, and butyl esters of 4-hydroxybenzoic acid, which indicate paraben hydrolase activity. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Effect of endophytic Bacillus cereus ERBP inoculation into non-native host: Potentials and challenges for airborne formaldehyde removal.

PubMed

Khaksar, Gholamreza; Treesubsuntorn, Chairat; Thiravetyan, Paitip

2016-10-01

Phytoremediation could be a cost-effective, environmentally friendly approach for the treatment of indoor air. However, some drawbacks still dispute the expediency of phytotechnology. Our objectives were to investigate the competency of plant growth-promoting (PGP) endophytic Bacillus cereus ERBP (endophyte root blue pea), isolated from the root of Clitoria ternatea, to colonize and stabilize within Zamioculcas zamiifolia and Euphorbia milii as non-native hosts without causing any disease or stress symptoms. Moreover, the impact of B. cereus ERBP on the natural shoot endophytic community and for the airborne formaldehyde removal capability of non-native hosts was assessed. Non-native Z. zamiifolia was effectively inoculated with B. cereus ERBP through soil as the most efficient method of endophyte inoculation. Denaturing gradient gel electrophoresis profiling of the shoot endophytic community verified the colonization and stability of B. cereus ERBP within its non-native host during a 20-d fumigation period without interfering with the natural shoot endophytic diversity of Z. zamiifolia. B. cereus ERBP conferred full protection to its non-native host against formaldehyde phytotoxicity and enhanced airborne formaldehyde removal of Z. zamiifolia whereas non-inoculated plants suffered from formaldehyde phytotoxicity because their natural shoot endophytic community was detrimentally affected by formaldehyde. In contrast, B. cereus ERBP inoculation into non-native E. milii deteriorated airborne formaldehyde removal of the non-native host (compared to a non-inoculated one) as B. cereus ERBP interfered with natural shoot endophytic community of E. milii, which caused stress symptoms and stimulated ethylene biosynthesis. Non-native host inoculation with PGP B. cereus ERBP could bear potentials and challenges for airborne formaldehyde removal. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Quantitative and qualitative measure of intralaboratory two-dimensional protein gel reproducibility and the effects of sample preparation, sample load, and image analysis.

PubMed

Choe, Leila H; Lee, Kelvin H

2003-10-01

We investigate one approach to assess the quantitative variability in two-dimensional gel electrophoresis (2-DE) separations based on gel-to-gel variability, sample preparation variability, sample load differences, and the effect of automation on image analysis. We observe that 95% of spots present in three out of four replicate gels exhibit less than a 0.52 coefficient of variation (CV) in fluorescent stain intensity (% volume) for a single sample run on multiple gels. When four parallel sample preparations are performed, this value increases to 0.57. We do not observe any significant change in quantitative value for an increase or decrease in sample load of 30% when using appropriate image analysis variables. Increasing use of automation, while necessary in modern 2-DE experiments, does change the observed level of quantitative and qualitative variability among replicate gels. The number of spots that change qualitatively for a single sample run in parallel varies from a CV = 0.03 for fully manual analysis to CV = 0.20 for a fully automated analysis. We present a systematic method by which a single laboratory can measure gel-to-gel variability using only three gel runs.

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

PubMed

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

2007-09-26

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

Evaluation of group A1B erythrocytes converted to type as group O: studies of markers of function and compatibility

PubMed Central

Gao, Hong-Wei; Zhuo, Hai-Long; Zhang, Xue; Ji, Shou-Ping; Tan, Ying-Xia; Li, Su-Bo; Jia, Yan-Jun; Xu, Hua; Wu, Qing-Fa; Yun, Zhi-Min; Luo, Qun; Gong, Feng

2016-01-01

Background Enzymatic conversion of blood group A1B red blood cells (RBC) to group O RBC (ECO) was achieved by combined treatment with α-galactosidase and α-N-acetylgalactosaminidase. The aim of this study was to evaluate the function and safety of these A1B-ECO RBC in vitro. Materials and methods A 20% packed volume of A1B RBC was treated with enzymes in 250 mM glycine buffer, pH 6.8. The efficiency of the conversion of A and B antigen was evaluated by traditional typing in test tubes, gel column agglutination technology and fluorescence-activated cell sorting (FACS) analysis. The physiological and metabolic parameters of native and ECO RBC were compared, including osmotic fragility, erythrocyte deformation index, levels of 2,3-diphosphoglycerate, ATP, methaemoglobin, free Na+, and free K+. The morphology of native and ECO RBC was observed by scanning electron microscopy. Residual α-galactosidase or α-N-acetylgalactosaminidase in A1B-ECO RBC was detected by double-antibody sandwich ELISA method. Manual cross-matching was applied to ensure blood compatibility. Results The RBC agglutination tests and FACS results showed that A1B RBC were efficiently converted to O RBC. Functional analysis suggested that the conversion process had little impact on the physiological and metabolic parameters of the RBC. The residual amounts of either α-galactosidase or α-N-acetylgalactosaminidase in the A1B-ECO RBC were less than 10 ng/mL of packed RBC. About 18% of group B and 55% of group O sera reacted with the A1B-ECO RBC in a sensitive gel column cross-matching test. Discussion The conversion process does not appear to affect the morphological, physiological or metabolic parameters of A1B-ECO RBC. However, the A1B-ECO RBC still reacted with some antigens. More research on group O and B sera, which may partly reflect the complexity of group A1 the safety of A1B-ECO RBC is necessary before the application of these RBC in clinical transfusion. PMID:26509826

Antioxidant enzymes expression in Pseudomonas aeruginosa exposed to UV-C radiation.

PubMed

Salma, Kloula Ben Ghorbal; Lobna, Maalej; Sana, Khefacha; Kalthoum, Chourabi; Imene, Ouzari; Abdelwaheb, Chatti

2016-07-01

It was well known that, UV-C irradiation increase considerably the reactive oxygen species (ROS) levels in eukaryotic and prokaryotic organisms. In the enzymatic ROS-scavenging pathways, superoxide dismutase (SOD), Catalase (CAT), and peroxidase (POX) were developed to deal with oxidative stress. In this study, we investigated the effects of UV-C radiations on antioxidant enzymes (catalase, superoxide dismutase, and peroxidases) expression in Pseudomonas aeruginosa. Catalase, superoxide dismutase, and peroxidases activities were determined spectrophotometrically. Isozymes of superoxide dismutase were revealed by native gel activity staining method. Lipid peroxidation was determined by measuring malondialdehyde formation. Our results showed that superoxide dismutase, catalase and peroxidase activities exhibited a gradual increase during the exposure time (30 min). However, the superoxide dismutase activity was maximized at 15 min. Native gel activity staining assays showed the presence of three superoxide dismutase isozymes. The iron-cofactored isoform activity was altered after exposure to UV-C stress. These finding suggest that catalase and peroxidase enzymes have the same importance toward UV-C rays at shorter and longer exposure times and this may confer additional protection to superoxide dismutase from damage caused by lipid peroxidation. Moreover, our data demonstrate the significant role of the antioxidant system in the resistance of this important human pathogen. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Low-resolution structure of Drosophila translin

PubMed Central

Kumar, Vinay; Gupta, Gagan D.

2012-01-01

Crystals of native Drosophila melanogaster translin diffracted to 7 Å resolution. Reductive methylation of the protein improved crystal quality. The native and methylated proteins showed similar profiles in size-exclusion chromatography analyses but the methylated protein displayed reduced DNA-binding activity. Crystals of the methylated protein diffracted to 4.2 Å resolution at BM14 of the ESRF synchrotron. Crystals with 49% solvent content belonged to monoclinic space group P21 with eight protomers in the asymmetric unit. Only 2% of low-resolution structures with similar low percentage solvent content were found in the PDB. The crystal structure, solved by molecular replacement method, refined to Rwork (Rfree) of 0.24 (0.29) with excellent stereochemistry. The crystal structure clearly shows that drosophila protein exists as an octamer, and not as a decamer as expected from gel-filtration elution profiles. The similar octameric quaternary fold in translin orthologs and in translin–TRAX complexes suggests an up-down dimer as the basic structural subunit of translin-like proteins. The drosophila oligomer displays asymmetric assembly and increased radius of gyration that accounts for the observed differences between the elution profiles of human and drosophila proteins on gel-filtration columns. This study demonstrates clearly that low-resolution X-ray structure can be useful in understanding complex biological oligomers. PMID:23650579

Purification of extensin from cell walls of tomato (hybrid of Lycopersicon esculentum and L. peruvianum) cells in suspension culture.

PubMed

Brownleader, M D; Dey, P M

1993-01-01

Extensin, a hydroxyproline-rich glycoprotein comprising substantial amounts of beta-L-arabinose-hydroxyproline glycosidic linkages is believed to be insolubilized in the cell wall during host-pathogen interaction by a peroxidase/hydroperoxide-mediated cross-linking process. Both extensin precursor and extensin peroxidase were ionically eluted from intact water-washed tomato (hybrid of Lycopersicon esculentum Mill. and L. peruvianum L. (Mill.) cells in suspension cultures and purified to homogeneity by a rapid and simple procedure under mild and non-destructive experimental conditions. The molecular weight of native extensin precursor was estimated to be greater than 240-300 kDa by Superose-12 gel-filtration chromatography. Extensin monomers have previously been designated a molecular weight of approximately 80 kDa. Our results indicate that salt-eluted extensin precursor is not monomeric. Agarose-gel electrophoresis, Superose-12-gel-filtration, extensin-peroxidase-catalysed cross-linking, Mono-S ion-exchange fast protein liquid chromatography (FPLC), and peptide-sequencing data confirmed the homogeneity of the extensin preparation. Evidence that the purified protein was extensin is attributed to the presence of the putative sequence motif--Ser (Hyp)4--within the N-terminal end of the protein. Treatment of extensin with trifluoroacetic acid demonstrated that arabinose was the principal carbohydrate. The amino-acid composition of the purified extensin was similar to those reported in the literature. The cross-linking of extensin in vitro upon incubation with extensin peroxidase and exogenous H2O2 was characteristic of other reported extensins. Furthermore, Mono-S ion-exchange FPLC of native extensin precursor resolved it into two isoforms, A (90%) and B (10%). The amino-acid compositions of extensin A and extensin B were found to be similar to each other and both extensins were cross-linked in vitro by extensin peroxidase.

Sensitive detection of influenza viruses with Europium nanoparticles on an epoxy silica sol-gel functionalized polycarbonate-polydimethylsiloxane hybrid microchip.

PubMed

Liu, Jikun; Zhao, Jiangqin; Petrochenko, Peter; Zheng, Jiwen; Hewlett, Indira

2016-12-15

In an effort to develop new tools for diagnosing influenza in resource-limited settings, we fabricated a polycarbonate (PC)-polydimethylsiloxane (PDMS) hybrid microchip using a simple epoxy silica sol-gel coating/bonding method and employed it in sensitive detection of influenza virus with Europium nanoparticles (EuNPs). The incorporation of sol-gel material in device fabrication provided functionalized channel surfaces ready for covalent immobilization of primary antibodies and a strong bonding between PDMS substrates and PC supports without increasing background fluorescence. In microchip EuNP immunoassay (µENIA) of inactivated influenza viruses, replacing native PDMS microchips with hybrid microchips allowed the achievement of a 6-fold increase in signal-to-background ratio, a 12-fold and a 6-fold decreases in limit-of-detection (LOD) in influenza A and B tests respectively. Using influenza A samples with known titers, the LOD of influenza µENIA on hybrid microchips was determined to be ~10(4) TCID50 titer/mL and 10(3)-10(4) EID50 titer/mL. A comparison test indicated that the sensitivity of influenza µENIA enhanced using the hybrid microchips even surpassed that of a commercial laboratory influenza ELISA test. In addition to the sensitivity improvement, assay variation was clearly reduced when hybrid microchips instead of native PDMS microchips were used in the µENIA tests. Finally, infectious reference viruses and nasopharyngeal swab patient specimens were successfully tested using μENIA on hybrid microchip platforms, demonstrating the potential of this unique microchip nanoparticle assay in clinical diagnosis of influenza. Meanwhile, the tests showed the necessity of using nucleic acid confirmatory tests to clarify ambiguous test results obtained from prototype or developed point-of-care testing devices for influenza diagnosis. Published by Elsevier B.V.

Instrumental texture profile analysis of gelatin gel extracted from grouper skin and commercial (bovine and porcine) gelatin gels.

PubMed

Rahman, Mohammad Shafiur; Al-Mahrouqi, Abdullah Issa

2009-01-01

Mechanical compression was used to study the gelling characteristics of gelatin gels. Texture profile analysis (TPA) showed that the hardness of fish and mammalian gelatin increased significantly as the concentrations of gels increased. TPA attributes of 10% fish skin gel showed significant differences from those obtained from 20% and 30% gels. In bovine and porcine cases, such generic trends were not observed. Mechanical characteristics of 10% gels of gelatin from fish skin, determined from one cycle compression, were significantly lower than other sources of gelatin gels, while bovine and porcine gels did not show any significant differences. In the case of TPA, hardness of bovine gelatin gel was highest at 41 N for 10% gel, followed by porcine (30 N) then fish skin (5 N) gelatin gels. The gels prepared from different sources did not show any generic trends when all other mechanical attributes were considered.

Drawing-induced changes in morphology and mechanical properties of hornet silk gel films.

PubMed

Kameda, Tsunenori; Kojima, Katsura; Togawa, Eiji; Sezutsu, Hideki; Zhang, Qiang; Teramoto, Hidetoshi; Tamada, Yasushi

2010-04-12

Complete amino acid sequences of the four major proteins (Vssilk 1-4) of silk (hornet silk) obtained from yellow hornet ( Vespa simillima , Vespinae, Vespidae) cocoons have been determined. The native structure of the hornet silk (HS), in which Vssilk 1-4 have an alpha-helix domain with coiled-coil alpha-helices and a beta-sheet domain, is restored when hornet silk gel films (HSGFs) are formed by pressing and drying HS hydrogel. Necking occurs when dry HSGFs are drawn; however, wet HSGFs can be uniaxially drawn with a draw ratio (DR) of 2. Drawing helps obtain high-performance films with a maximum tensile strength and tensile modulus of 170 MPa and 5.5 GPa, respectively. Drawing-induced changes in the orientation and conformation of the coiled-coil structure are investigated.

Studies on lectins. XXXII. Application of affinity electrophoresis to the study of the interaction of lectins and their derivatives with sugars.

PubMed

Horejsí, V; Tichá, M; Kocourek, J

1977-09-29

Affinity electrophoresis was used to study the sugar binding heterogeneity of lectins or their derivatives. Commercial and demetallized preparations of concanavalin A could be resolved by affinity electrophoresis into three components with different affinity to immobilized sugar. Similarly the Vicia cracca lectin obtained by affinity chromatography behaved on affinity gels as a mixture of active and inactive molecular species. Affinity electrophoresis has shown that the nonhemagglutinating acetylated lentil lectin and photo-oxidized or sulfenylated pea lectin retain their sugar binding properties; dissociation constants of saccharide complexes of these derivatives are similar to those of native lectins. The presence of specific immobilized sugar in the affinity gel improved the resolution of isolectins from Dolichos biflorus and Ricinus communis seeds.

A Routine 'Top-Down' Approach to Analysis of the Human Serum Proteome.

PubMed

D'Silva, Arlene M; Hyett, Jon A; Coorssen, Jens R

2017-06-06

Serum provides a rich source of potential biomarker proteoforms. One of the major obstacles in analysing serum proteomes is detecting lower abundance proteins owing to the presence of hyper-abundant species (e.g., serum albumin and immunoglobulins). Although depletion methods have been used to address this, these can lead to the concomitant removal of non-targeted protein species, and thus raise issues of specificity, reproducibility, and the capacity for meaningful quantitative analyses. Altering the native stoichiometry of the proteome components may thus yield a more complex series of issues than dealing directly with the inherent complexity of the sample. Hence, here we targeted method refinements so as to ensure optimum resolution of serum proteomes via a top down two-dimensional gel electrophoresis (2DE) approach that enables the routine assessment of proteoforms and is fully compatible with subsequent mass spectrometric analyses. Testing included various fractionation and non-fractionation approaches. The data show that resolving 500 µg protein on 17 cm 3-10 non-linear immobilised pH gradient strips in the first dimension followed by second dimension resolution on 7-20% gradient gels with a combination of lithium dodecyl sulfate (LDS) and sodium dodecyl sulfate (SDS) detergents markedly improves the resolution and detection of proteoforms in serum. In addition, well established third dimension electrophoretic separations in combination with deep imaging further contributed to the best available resolution, detection, and thus quantitative top-down analysis of serum proteomes.

Oxidative stress induction by Prunus necrotic ringspot virus infection in apricot seeds.

PubMed

Amari, Khalid; Díaz-Vivancos, Pedro; Pallás, Vincente; Sánchez-Pina, María Amelia; Hernández, José Antonio

2007-10-01

Prunus necrotic ringspot rvirus (PNRSV) was able to invade the immature apricot seed including the embryo. The amount of virus was very high inside the embryo compared with that present in the cotyledons. PNRSV infection produced an oxidative stress in apricot seeds as indicated by the increase in lipid peroxidation, measured as thiobarbituric acid-reactive substances. This lipid peroxidation increase was parallelled with an imbalance in the seed antioxidant enzymes. A significant decrease in the ascorbate-GSH cycle enzymes as well as in peroxidase (POX) activity took place in infected seeds, suggesting a low capability to eliminate H2O2. No changes in superoxide dismutase (SOD) or catalase activity were observed. A significant decrease in polyphenoloxidase (PPO) activity was also observed. Native PAGE revealed the presence of three different SOD activity bands in apricot seeds: a Mn-containing SOD and two CuZn-containing SODs. Only an isozyme with catalase, glutathione reductase (GR) or PPO activity was detected in both healthy and infected apricot seeds. Regarding POX staining, three bands with POX activity were detected in native gels in both healthy and infected seeds. The gel results emphasise that the drop detected in POX, GR and PPO activities in PNRSV-infected apricot seeds by kinetic analyses was also evident from the results obtained by native PAGE. The oxidative stress and the imbalance in the antioxidant systems from PNRSV-infected apricot seeds resemble the hypersensitive response observed in some virus-host interactions. This defence mechanism would inactivate PNRSV during seed formation and/or the storage period or even during seed germination. Those results can explain the decrease in seed germination and the low transmission of PNRSV by seeds in apricot trees.

Mold Pectinase Modified with Dialdehyde Derivatives of Dextran and Cellulose.

PubMed

Kobayashi, M; Chiba, Y; Funane, K; Ohya, S; Kato, Y

1996-01-01

Chemical modification of mold pectinase with dextran- and cellulose-dialdehydes was examined to improve the enzyme characteristics. The modified pectinase with dextran-dialdehyde retained about 50% of the original activity, and more than 80% of the total amino groups were modified. HPLC gel filtration analysis showed an increase in molecular weight of the reaction product. Reaction with cellulose-dialdehyde provided an immobilized form of pectinase. The immobilized pectinase was resistant to both acidic and alkaline pHs, and also acquired heat stability at 60°C. The optimum pH of the modified enzyme shifted from pH 4.5 to 5.0-5.5, and this enzyme had higher activity at neutral pH regions than the native enzyme. A rather low recovery of immobilized enzyme (14.5%) should be improved by the combination with various methods hitherto established.

Purification and characterization of a serine protease (CPM-2) with fibrinolytic activity from the dung beetles.

PubMed

Ahn, Mi Young; Hahn, Bum-Soo; Ryu, Kang Sun; Hwang, Jae Sam; Kim, Yeong Shik

2005-07-01

Catharsius protease-2 (CPM-2) was isolated from the body of dung beetles, Catharsius molossus, using a three step purification process (ammonium sulfate fractionation, gel filtration on Bio-Gel P-60, and affinity chromatography on DEAE Affi-Gel blue). The purified CPM-2, having a molecular weight of 24 kDa, was assessed homogeneously by SDS-polyacrylamide gel electrophoresis. The N-terminal amino acid sequence of CPM-2 was composed of X Val Gln Asp Phe Val Glu Glu Ile Leu. CPM-2 was inactivated by Cu2+ and Zn2+ and strongly inhibited by typical serine proteinase inhibitors such as TLCK, soybean trypsin inhibitor, aprotinin, benzamidine, and alpha1-antitrypsin. However, EDTA, EGTA, cysteine, beta-mercaptoethanol, E64, and elastatinal had little effect on enzyme activity. In addition, antiplasmin and antithrombin III were not sensitive to CPM-2. Based on the results of a fibrinolytic activity test, CPM-2 readily cleaved Aalpha- and Bbeta-chains of fibrinogen and fibrin, and gamma-chain of fibrinogen more slowly. The nonspecific action of the enzyme resulted in extensive hydrolysis, releasing a variety of fibrinopeptides of fibrinogen and fibrin. Polyclonal antibodies of CPM-2 were reactive to the native form of antigen. The ELISA was applied to detect quantities, in nanograms, of the antigen in CPM-2 protein.

Three RNases in Senescent and Nonsenescent Wheat Leaves 1

PubMed Central

Blank, A.; McKeon, Thomas A.

1991-01-01

We have described three RNases in wheat leaves (Triticum aestivum L. cv Chinese Spring) and developed assays for measuring each RNase individually in crude leaf extracts. We initially used activity staining in sodium dodecyl sulfate-polyacrylamide gels to characterize RNases in extracts of primary and flag leaves. We thus identified acid RNase (EC 3.1.27.1, here designated RNase WLA), and two apparently novel enzymes, designated RNases WLB and WLC. RNase WLB activity displays a distinctive isozyme pattern, a molecular mass of 26 kilodaltons (major species), a broad pH range with an optimum near neutrality, insensitivity to EDTA, and stimulation by moderate concentrations of KCl and by MgCl2. RNase WLC activity exhibits a molecular mass of 27 kilodaltons, a neutral pH optimum, insensitivity to EDTA, and inhibition by KCl, MgCl2, and tri-(hydroxymethyl)aminomethane. Based on distinctive catalytic properties established in gels, we designed conventional solution assays for selective quantitation of each RNase activity. We used the assays to monitor the individual RNases after gel filtration chromatography and native gel electrophoresis of extracts. In accompanying work, we used the assays to monitor RNases WLA, WLB, and WLC, which are present in senescent and nonsenescent leaves, during the course of leaf senescence. ImagesFigure 1Figure 3Figure 4 PMID:16668563

Isolation and characterization of a mannan from mesosomal membrane vesicles of Micrococcus lysodeikticus.

PubMed

Owen, P; Salton, M R

1975-10-06

The carbohydrate content of mesosomal membranes of Micrococcus lysodeikticus has been shown to be consistently higher (about four times) than that of corresponding plasma membrane preparations. Analysis of washed membrane fractions by gas-liquid chromatography indicated that mannose was the major neutral sugar of both types of membrane (accounting for 95 and 89%, respectively, of the mesosomal and plasma membrane carbohydrate). Small amounts of inositol, glucose and ribose were also detected. We have shown by polyacrylamide gel electrophoresis in sodium dodecylsulphate and by precipitation and agar gel diffusion experiments with concanavalin A that a mannan is the major carbohydrate component of both types of membrane. This polymer can be selectively released from mesosomal membranes by a simple procedure involving low ionic strength-shock and heating to 80 degrees C for 1 min, and purified by ultrafiltration and ethanol precipitation. The mannan contains mannose as the only neutral carbohydrate, is not phosphorylated and does not contain significant amounts of amino sugars or uronic acids. Agar gel electrophoresis experiments, however, indicate an anionic polymer whose acidic properties are eliminated upon mild base hydrolysis. Analysis of native mannan by infrared spectroscopy reveals absorption bands attributable to ester carbonyl groups and to carboxylate ions, consistent with the presence of succinyl residues in the polymer (Owen, P. and Salton, M.R.J. (1975) Biochem, Biophys. Res. Commun. 63, 875--800). A sedimentation coefficient of 1.39 S was obtained by analytical ultracentrifugation in 1.0 M NaCl and a value of one reducing equivalent per 50 mannose residues by reduction with NaB3H4. The polysaccharide was only slightly degraded (2%) by jack bean alpha-mannosidase and could precipitate 15 times its own weight of concanavalin A. The acidic polymers was also detected in the cell "periplasm" and was secreted from cells grown in defined media during the period of decelerating growth.

Surface charge dependent separation of modified and hybrid ferritin in native PAGE: Impact of lysine 104.

PubMed

Subhadarshanee, Biswamaitree; Mohanty, Abhinav; Jagdev, Manas Kumar; Vasudevan, Dileep; Behera, Rabindra K

2017-10-01

Preparation of modified and hybrid ferritin provides a great opportunity to understand the mechanisms of iron loading/unloading, protein self-assembly, size constrained nanomaterial synthesis and targeted drug delivery. However, the large size (M.W.=490kDa) has been limiting the separation of different modified and/or hybrid ferritin nanocages from each other in their intact assembled form and further characterization. Native polyacrylamide gel electrophoresis (PAGE) separates proteins on the basis of both charge and mass, while maintaining their overall native structure and activity. Altering surface charge distribution by substitution of amino acid residues located at the external surface of ferritin (K104E & D40A) affected the migration rate in native PAGE while internal modification had little effect. Crystal structures confirmed that ferritin nanocages made up of subunits with single amino acid substitutions retain the overall structure of ferritin nanocage. Taking advantage of K104E migration behavior, formation of hybrid ferritins with subunits of wild type (WT) and K104E were confirmed and separated in native PAGE. Cage integrity and iron loading ability (ferritin activity) were also tested. The migration pattern of hybrid ferritins in native PAGE depends on the subunit ratio (WT: K104E) in the ferritin cage. Our work shows that native PAGE can be exploited in nanobiotechnology, by analyzing modifications of large proteins like ferritin. Native PAGE, a simple, straight-forward technique, can be used to analyze small modification (by altering external surface charge) in large proteins like ferritin, without disintegrating its self-assembled nanocage structure. In doing so, native PAGE can complement the information obtained from mass spectrometry. The confirmation and separation of modified and hybrid ferritin protein nanocages in native PAGE, opens up various prospects of bio-conjugation, which can be useful in targeted drug delivery, nanobiotechnology and in understanding nature's idea of synthesizing hybrid ferritins in different human tissues. Copyright © 2017 Elsevier B.V. All rights reserved.

Ndufs4 related Leigh syndrome: A case report and review of the literature.

PubMed

Ortigoza-Escobar, Juan Darío; Oyarzabal, Alfonso; Montero, Raquel; Artuch, Rafael; Jou, Cristina; Jiménez, Cecilia; Gort, Laura; Briones, Paz; Muchart, Jordi; López-Gallardo, Ester; Emperador, Sonia; Pesini, Eduardo Ruiz; Montoya, Julio; Pérez, Belén; Rodríguez-Pombo, Pilar; Pérez-Dueñas, Belén

2016-05-01

The genetic causes of Leigh syndrome are heterogeneous, with a poor correlation between the phenotype and genotype. Here, we present a patient with an NDUFS4 mutation to expand the clinical and biochemical spectrum of the disease. A combined defect in the CoQ, PDH and RCC activities in our patient was due to an inappropriate assembly of the RCC complex I (CI), which was confirmed using Blue-Native polyacrylamide gel electrophoresis (BN-PAGE) analysis. Targeted exome sequencing analysis allowed for the genetic diagnosis of this patient. We reviewed 198 patients with 24 different genetic defects causing RCC I deficiency and compared them to 22 NDUFS4 patients. We concluded that NDUFS4-related Leigh syndrome is invariably linked to an early onset severe phenotype that results in early death. Some data, including the clinical phenotype, neuroimaging and biochemical findings, can guide the genetic study in patients with RCC I deficiency. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Effects of phosphate-solubilizing bacteria, native microorganisms, and rock dust on Jatropha curcas L. growth.

PubMed

Santana, E B; Marques, E L S; Dias, J C T

2016-10-05

Microorganisms with the ability to release nutrients to the soil from insoluble sources may be useful for plant cultivation. We evaluated the growth-promoting effect on Jatropha curcas L. of phosphate-solubilizing bacteria (PSB) and the native microbiota in soil with or without rock dust. J. curcas L. is important for biodiesel production. The experiments were performed in a greenhouse under a random-statistical design with 14 replicates. The soil received increasing dosages of rock dust. The presence of resident microorganisms and PSB inoculum was correlated with plant height, biomass production, and phosphorus content in plants for 120 days. Native soil microorganisms were detected and identified using denaturing gradient gel electrophoresis and DNA sequence analysis. Several bacterial populations belonged to the genus Bacillus. Populations associated with the phyla Chytridiomycota and Ascomycota were detected among the fungi. The best results for the variable plant height were correlated with the presence of resident microbiota and rock dust until the end of the experiment. The largest biomass production and the highest content of phosphorus occurred in the presence of soil-resident microbiota only up to 120 days. No significant effects were observed for biomass production with the use of PSB combined with rock dust. J. curcas L. under the influence of only resident microbiota showed the best plant growth results. Future research will focus on the specificity of resident microbiota activity in plant growth promotion and the isolation of these microorganisms to produce a new inoculum to be tested in various plants.

Spider Silk-CBD-Cellulose Nanocrystal Composites: Mechanism of Assembly

PubMed Central

Meirovitch, Sigal; Shtein, Zvi; Ben-Shalom, Tal; Lapidot, Shaul; Tamburu, Carmen; Hu, Xiao; Kluge, Jonathan A.; Raviv, Uri; Kaplan, David L.; Shoseyov, Oded

2016-01-01

The fabrication of cellulose-spider silk bio-nanocomposites comprised of cellulose nanocrystals (CNCs) and recombinant spider silk protein fused to a cellulose binding domain (CBD) is described. Silk-CBD successfully binds cellulose, and unlike recombinant silk alone, silk-CBD self-assembles into microfibrils even in the absence of CNCs. Silk-CBD-CNC composite sponges and films show changes in internal structure and CNC alignment related to the addition of silk-CBD. The silk-CBD sponges exhibit improved thermal and structural characteristics in comparison to control recombinant spider silk sponges. The glass transition temperature (Tg) of the silk-CBD sponge was higher than the control silk sponge and similar to native dragline spider silk fibers. Gel filtration analysis, dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (TEM) indicated that silk-CBD, but not the recombinant silk control, formed a nematic liquid crystalline phase similar to that observed in native spider silk during the silk spinning process. Silk-CBD microfibrils spontaneously formed in solution upon ultrasonication. We suggest a model for silk-CBD assembly that implicates CBD in the central role of driving the dimerization of spider silk monomers, a process essential to the molecular assembly of spider-silk nanofibers and silk-CNC composites. PMID:27649169

Reconstitution of the Escherichia coli pyruvate dehydrogenase complex.

PubMed Central

Reed, L J; Pettit, F H; Eley, M H; Hamilton, L; Collins, J H; Oliver, R M

1975-01-01

The binding of pyruvate dehydrogenase and dihydrolipoyl dehydrogenase (flavoprotein) to dihydrolipoyl transacetylase, the core enzyme of the E. coli pyruvate dehydrogenase complex [EC 1.2.4.1:pyruvate:lipoate oxidoreductase (decaryboxylating and acceptor-acetylating)], has been studied using sedimentation equilibrium analysis and radioactive enzymes in conjunction with gel filtration chromatography. The results show that the transacetylase, which consists of 24 apparently identical polypeptide chains organized into a cube-like structure, has the potential to bind 24 pyruvate dehydrogenase dimers in the absence of flavoprotein and 24 flavoprotein dimers in the absence of pyruvate dehydrogenase. The results of reconstitution experiments, utilizing binding and activity measurements, indicate that the transacetylase can accommodate a total of only about 12 pyruvate dehydrogenase dimers and six flavoprotein dimers and that this stoichiometry, which is the same as that of the native pyruvate dehydrogenase complex, produces maximum activity. It appears that steric hindrance between the relatively bulky pyruvate dehydrogenase and flavoprotein molecules prevents the transacetylase from binding 24 molecules of each ligand. A structural model for the native and reconstituted pyruvate dehydrogenase complexes is proposed in which the 12 pyruvate dehydrogenase dimers are distributed symmetrically on the 12 edges of the transacetylase cube and the six flavoprotein dimers are distributed in the six faces of the cube. Images PMID:1103138

Characterization of pancreatic lipase-related protein 2 isolated from human pancreatic juice.

PubMed

De Caro, Josiane; Sias, Barbara; Grandval, Philippe; Ferrato, Francine; Halimi, Hubert; Carrière, Frédéric; De Caro, Alain

2004-09-01

Human pancreatic lipase-related protein 2 (HPLRP2) was identified for the first time in pancreatic juice using specific anti-peptide antibodies and purified to homogeneity. Antibodies were raised in the rabbit using a synthetic peptide from the HPLRP2 protein sequence deduced from cDNA. Western blotting analysis showed that these antibodies did not react with classical human pancreatic lipase (HPL) or human pancreatic lipase-related protein 1 (HPLRP1) but cross-reacted with native rat PLRP2 (RPLRP2), as well as with recombinant rat and guinea-pig PLRP2 (GPLRP2). Immunoaffinity chromatography was performed on immobilized anti-recombinant HPLRP2 polyclonal antibodies to purify native HPLRP2 after conventional chromatographic steps including gel filtration and chromatrography on an anion-exchanger. The substrate specificity of HPLRP2 was investigated using various triglycerides, phospholipids and galactolipids as substrates. The lipase activity on triglycerides was inhibited by bile salts and weakly restored by colipase. The phospholipase activity of HPLRP2 on phospholipid micelles was very low. A significant level of galactolipase activity was measured using monogalactosyldiglyceride monomolecular films. These data suggest that the main physiological function of HPLRP2 is the hydrolysis of galactolipids, which are the main lipids present in vegetable food.

Spider Silk-CBD-Cellulose Nanocrystal Composites: Mechanism of Assembly.

PubMed

Meirovitch, Sigal; Shtein, Zvi; Ben-Shalom, Tal; Lapidot, Shaul; Tamburu, Carmen; Hu, Xiao; Kluge, Jonathan A; Raviv, Uri; Kaplan, David L; Shoseyov, Oded

2016-09-18

The fabrication of cellulose-spider silk bio-nanocomposites comprised of cellulose nanocrystals (CNCs) and recombinant spider silk protein fused to a cellulose binding domain (CBD) is described. Silk-CBD successfully binds cellulose, and unlike recombinant silk alone, silk-CBD self-assembles into microfibrils even in the absence of CNCs. Silk-CBD-CNC composite sponges and films show changes in internal structure and CNC alignment related to the addition of silk-CBD. The silk-CBD sponges exhibit improved thermal and structural characteristics in comparison to control recombinant spider silk sponges. The glass transition temperature (Tg) of the silk-CBD sponge was higher than the control silk sponge and similar to native dragline spider silk fibers. Gel filtration analysis, dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (TEM) indicated that silk-CBD, but not the recombinant silk control, formed a nematic liquid crystalline phase similar to that observed in native spider silk during the silk spinning process. Silk-CBD microfibrils spontaneously formed in solution upon ultrasonication. We suggest a model for silk-CBD assembly that implicates CBD in the central role of driving the dimerization of spider silk monomers, a process essential to the molecular assembly of spider-silk nanofibers and silk-CNC composites.

Improved quality of cartilage repair by bone marrow mesenchymal stem cells for treatment of an osteochondral defect in a cynomolgus macaque model

PubMed Central

Araki, Susumu; Imai, Shinji; Ishigaki, Hirohito; Mimura, Tomohiro; Nishizawa, Kazuya; Ueba, Hiroaki; Kumagai, Kousuke; Kubo, Mitsuhiko; Mori, Kanji; Ogasawara, Kazumasa; Matsusue, Yoshitaka

2015-01-01

Background and purpose Integration of repaired cartilage with surrounding native cartilage is a major challenge for successful tissue-engineering strategies of cartilage repair. We investigated whether incorporation of mesenchymal stem cells (MSCs) into the collagen scaffold improves integration and repair of cartilage defects in a cynomolgus macaque model. Methods Cynomolgus macaque bone marrow-derived MSCs were isolated and incorporated into type-I collagen gel. Full-thickness osteochondral defects (3 mm in diameter, 5 mm in depth) were created in the patellar groove of 36 knees of 18 macaques and were either left untreated (null group, n = 12), had collagen gel alone inserted (gel group, n = 12), or had collagen gel incorporating MSCs inserted (MSC group, n = 12). After 6, 12, and 24 weeks, the cartilage integration and tissue response were evaluated macroscopically and histologically (4 null, 4 gel, and 4 MSC knees at each time point). Results The gel group showed most cartilage-rich reparative tissue covering the defect, owing to formation of excessive cartilage extruding though the insufficient subchondral bone. Despite the fact that a lower amount of new cartilage was produced, the MSC group had better-quality cartilage with regular surface, seamless integration with neighboring naïve cartilage, and reconstruction of trabecular subchondral bone. Interpretation Even with intensive investigation, MSC-based cell therapy has not yet been established in experimental cartilage repair. Our model using cynomolgus macaques had optimized conditions, and the method using MSCs is superior to other experimental settings, allowing the possibility that the procedure might be introduced to future clinical practice. PMID:25175660

Pyrene-based fluorescent ambidextrous gelators: scaffolds for mechanically robust SWNT-gel nanocomposites.

PubMed

Mandal, Deep; Kar, Tanmoy; Das, Prasanta Kumar

2014-01-27

With the rapid progress in the development of supramolecular soft materials, examples of low-molecular-weight gelators (LMWGs) with the ability to immobilise both water and organic solvents by the same structural scaffold are very limited. In this paper, we report the development of pyrene-containing peptide-based ambidextrous gelators (AGs) with the ability to efficiently gelate both organic and aqueous solvents. The organo- and hydrogelation efficiencies of these gelators are in the range 0.7-1.1% w/v in various organic solvents and 0.5-5% w/v in water at certain acidic pH values (pH 2.0-4.0). Moreover, for the first time, AGs have been utilised to prepare single-walled carbon-nanotube (SWNT)-included soft nanocomposites in both hydro- and organogel matrices. The influence of different non-covalent interactions such as hydrogen bonding, hydrophobic, π-π and van der Waals interactions in self-assembled gelation has been studied in detail by circular dichroism, FTIR, variable-temperature NMR, 2D NOESY and luminescence spectroscopy. Interestingly, the presence of the pyrene moiety in the structure rendered these AGs intrinsically fluorescent, which was quenched upon successful integration of the SWNTs within the gel. The prepared hydro- and organogels along with their SWNT-integrated nanocomposites are thermoreversible in nature. The supramolecular morphologies of the dried gels and SWNT-gel nanocomposites have been studied by transmission electron microscopy, fluorescence microscopy and polarising optical microscopy, which confirmed the presence of three-dimensional self-assembled fibrillar networks (SAFINs) as well as the integrated SWNTs. Importantly, rheological studies revealed that the inclusion of SWNTs within the ambidextrous gels improved the mechanical rigidity of the resulting soft nanocomposites up to 3.8-fold relative to the native gels. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stoichiometry of DNA binding by the bacteriophage SP01-encoded type II DNA-binding protein TF1.

PubMed

Schneider, G J; Geiduschek, E P

1990-06-25

The stoichiometry of DNA binding by the bacteriophage SP01-encoded type II DNA-binding protein TF1 has been determined. 3H-Labeled TF1 was allowed to bind to a 32P-labeled DNA fragment containing a TF1 binding site. Multiple TF1-DNA complexes were resolved from each other and from unbound DNA by native gel electrophoresis. DNA-protein complexes were cut from polyacrylamide gels, and the amounts of 3H and 32P contained in each slice were measured. A ratio of 1.12 +/- 0.06 TF1 dimer/DNA molecule was calculated for the fastest-migrating TF1-DNA complex. We conclude that TF1 has a DNA-binding unit of one dimer. More slowly migrating complexes are apparently formed by serial addition of single TF1 dimers.

Integration of motor proteins - towards an ATP fueled soft actuator.

PubMed

Kakugo, Akira; Shikinaka, Kazuhiro; Gong, Jian Ping

2008-09-01

We present a soft bio-machine constructed from biological motors (actin/myosin). We have found that chemically cross-linked polymer-actin complex gel filaments can move on myosin coated surfaces with a velocity as high as that of native F-actin, by coupling to ATP hydrolysis. Additionally, it is shown that the velocity of polymer-actin complex gel depends on the species of polycations binding to the F-actins. Since the design of functional actuators of well-defined size and morphology is important, the structural behavior of polymer-actin complexes has been investigated. Our results show that the morphology and growth size of polymer-actin complex can be controlled by changes in the electrostatic interactions between F-actins and polycations. Our results indicate that bio actuators with desired shapes can be created by using a polymer-actin complex.

Anomalous NMR Relaxation in Cartilage Matrix Components and Native Cartilage: Fractional-Order Models

PubMed Central

Magin, Richard L.; Li, Weiguo; Velasco, M. Pilar; Trujillo, Juan; Reiter, David A.; Morgenstern, Ashley; Spencer, Richard G.

2011-01-01

We present a fractional-order extension of the Bloch equations to describe anomalous NMR relaxation phenomena (T1 and T2). The model has solutions in the form of Mittag-Leffler and stretched exponential functions that generalize conventional exponential relaxation. Such functions have been shown by others to be useful for describing dielectric and viscoelastic relaxation in complex, heterogeneous materials. Here, we apply these fractional-order T1 and T2 relaxation models to experiments performed at 9.4 and 11.7 Tesla on type I collagen gels, chondroitin sulfate mixtures, and to bovine nasal cartilage (BNC), a largely isotropic and homogeneous form of cartilage. The results show that the fractional-order analysis captures important features of NMR relaxation that are typically described by multi-exponential decay models. We find that the T2 relaxation of BNC can be described in a unique way by a single fractional-order parameter (α), in contrast to the lack of uniqueness of multi-exponential fits in the realistic setting of a finite signal-to-noise ratio. No anomalous behavior of T1 was observed in BNC. In the single-component gels, for T2 measurements, increasing the concentration of the largest components of cartilage matrix, collagen and chondroitin sulfate, results in a decrease in α, reflecting a more restricted aqueous environment. The quality of the curve fits obtained using Mittag-Leffler and stretched exponential functions are in some cases superior to those obtained using mono- and bi-exponential models. In both gels and BNC, α appears to account for microstructural complexity in the setting of an altered distribution of relaxation times. This work suggests the utility of fractional-order models to describe T2 NMR relaxation processes in biological tissues. PMID:21498095

Integration of isoelectric focusing with parallel sodium dodecyl sulfate gel electrophoresis for multidimensional protein separations in a plastic microfluidic [correction of microfludic] network.

PubMed

Li, Yan; Buch, Jesse S; Rosenberger, Frederick; DeVoe, Don L; Lee, Cheng S

2004-02-01

An integrated protein concentration/separation system, combining non-native isoelectric focusing (IEF) with sodium dodecyl sulfate (SDS) gel electrophoresis on a polymer microfluidic chip, is reported. The system provides significant analyte concentration and extremely high resolving power for separated protein mixtures. The ability to introduce and isolate multiple separation media in a plastic microfluidic network is one of two key requirements for achieving multidimensional protein separations. The second requirement lies in the quantitative transfer of focused proteins from the first to second separation dimensions without significant loss in the resolution acquired from the first dimension. Rather than sequentially sampling protein analytes eluted from IEF, focused proteins are electrokinetically transferred into an array of orthogonal microchannels and further resolved by SDS gel electrophoresis in a parallel and high-throughput format. Resolved protein analytes are monitored using noncovalent, environment-sensitive, fluorescent probes such as Sypro Red. In comparison with covalently labeling proteins, the use of Sypro staining during electrophoretic separations not only presents a generic detection approach for the analysis of complex protein mixtures such as cell lysates but also avoids additional introduction of protein microheterogeneity as the result of labeling reaction. A comprehensive 2-D protein separation is completed in less than 10 min with an overall peak capacity of approximately 1700 using a chip with planar dimensions of as small as 2 cm x 3 cm. Significant enhancement in the peak capacity can be realized by simply raising the density of microchannels in the array, thereby increasing the number of IEF fractions further analyzed in the size-based separation dimension.

Anomalous NMR relaxation in cartilage matrix components and native cartilage: Fractional-order models

NASA Astrophysics Data System (ADS)

Magin, Richard L.; Li, Weiguo; Pilar Velasco, M.; Trujillo, Juan; Reiter, David A.; Morgenstern, Ashley; Spencer, Richard G.

2011-06-01

We present a fractional-order extension of the Bloch equations to describe anomalous NMR relaxation phenomena ( T1 and T2). The model has solutions in the form of Mittag-Leffler and stretched exponential functions that generalize conventional exponential relaxation. Such functions have been shown by others to be useful for describing dielectric and viscoelastic relaxation in complex, heterogeneous materials. Here, we apply these fractional-order T1 and T2 relaxation models to experiments performed at 9.4 and 11.7 Tesla on type I collagen gels, chondroitin sulfate mixtures, and to bovine nasal cartilage (BNC), a largely isotropic and homogeneous form of cartilage. The results show that the fractional-order analysis captures important features of NMR relaxation that are typically described by multi-exponential decay models. We find that the T2 relaxation of BNC can be described in a unique way by a single fractional-order parameter ( α), in contrast to the lack of uniqueness of multi-exponential fits in the realistic setting of a finite signal-to-noise ratio. No anomalous behavior of T1 was observed in BNC. In the single-component gels, for T2 measurements, increasing the concentration of the largest components of cartilage matrix, collagen and chondroitin sulfate, results in a decrease in α, reflecting a more restricted aqueous environment. The quality of the curve fits obtained using Mittag-Leffler and stretched exponential functions are in some cases superior to those obtained using mono- and bi-exponential models. In both gels and BNC, α appears to account for micro-structural complexity in the setting of an altered distribution of relaxation times. This work suggests the utility of fractional-order models to describe T2 NMR relaxation processes in biological tissues.

Hydrodynamic properties of porcine bestrophin-1 in Triton X-100.

PubMed

Stanton, J Brett; Goldberg, Andrew F X; Hoppe, George; Marmorstein, Lihua Y; Marmorstein, Alan D

2006-02-01

Bestrophin-1 (Best-1) is an integral membrane protein, defects in which cause Best vitelliform macular dystrophy. Best-1 is proposed to function as a Cl- channel and/or a regulator of Ca++ channels. A tetrameric (or pentameric) stoichiometry has been reported for recombinant best-1. Using a combination of gel exclusion chromatography and velocity sedimentation we examined the quaternary structure of native best-1 and found that it migrates as a single species with a Stokes radius of 7.3 nm, sedimentation coefficient (S20,w) of 4.9, and partial specific volume (nu) of 0.80 ml/g. The mass of the protein-detergent complex is calculated to be 206 kDa, with the protein component estimated to be approximately 138 kDa. Given a monomeric mass of 68 kDa, we conclude that native best-1 solubilized with Triton X-100 is a homodimer. The differences between this observation and a prior report were examined by comparing recombinant best-1 with tissue derived best-1 using gel exclusion chromatography. Much of the recombinant best-1 eluted in the column void (Vo) fraction, unlike that extracted from RPE cells. We conclude that the minimal functional unit of best-1 is dimeric. This stoichiometry differs from that previously measured for recombinant best-1, suggesting that further studies are necessary to determine the stoichiometry of functional best-1 in RPE membranes.

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

PubMed

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

1990-01-01

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

Influence of heat and shear induced protein aggregation on the in vitro digestion rate of whey proteins.

PubMed

Singh, Tanoj K; Øiseth, Sofia K; Lundin, Leif; Day, Li

2014-11-01

Protein intake is essential for growth and repair of body cells, the normal functioning of muscles, and health related immune functions. Most food proteins are consumed after undergoing various degrees of processing. Changes in protein structure and assembly as a result of processing impact the digestibility of proteins. Research in understanding to what extent the protein structure impacts the rate of proteolysis under human physiological conditions has gained considerable interest. In this work, four whey protein gels were prepared using heat processing at two different pH values, 6.8 and 4.6, with and without applied shear. The gels showed different protein network microstructures due to heat induced unfolding (at pH 6.8) or lack of unfolding, thus resulting in fine stranded protein networks. When shear was applied during heating, particulate protein networks were formed. The differences in the gel microstructures resulted in considerable differences in their rheological properties. An in vitro gastric and intestinal model was used to investigate the resulting effects of these different gel structures on whey protein digestion. In addition, the rate of digestion was monitored by taking samples at various time points throughout the in vitro digestion process. The peptides in the digesta were profiled using SDS-polyacrylamide gel electrophoresis, reversed-phase-HPLC and LC-MS. Under simulated gastric conditions, whey proteins in structured gels were hydrolysed faster than native proteins in solution. The rate of peptides released during in vitro digestion differed depending on the structure of the gels and extent of protein aggregation. The outcomes of this work highlighted that changes in the network structure of the protein can influence the rate and pattern of its proteolysis under gastrointestinal conditions. Such knowledge could assist the food industry in designing novel food formulations to control the digestion kinetics and the release of biologically active peptides for desired health outcome.

The Impact of HA Oligomer Content on Physical, Mechanical, and Biologic Properties of Divinyl Sulfone-Crosslinked HA Hydrogels

PubMed Central

Ibrahim, Samir; Kang, Qian K; Ramamurthi, Anand

2009-01-01

In recent studies, we showed that exogenous hyaluronic acid oligomers (HA-o) stimulate functional endothelialization, though native long-chain HA is more bioinert and possibly more biocompatible. Thus, in this study, hydrogels containing high molecular weight (HMW) HA (1×106 Da) and HA oligomer mixtures (HA-o: 0.75–10 kDa) were created by crosslinking with divinyl sulfone (DVS). The incorporation of HA oligomers was found to compromise the physical and mechanical properties of the gels (rheology, apparent crosslinking density, swelling ratio, degradation) and to very mildly enhance inflammatory cell recruitment in vivo; increasing the DVS crosslinker content within the gels in general, had the opposite effect, though the relatively high concentration of DVS within these gels (necessary to create a solid gel) also stimulated a mild sub-cutaneous inflammatory response in vivo and VCAM-1 expression by ECs cultured atop; ICAM-expression levels remained very low irrespective extent of DVS crosslinking or HA-o content. The greatest EC attachment and proliferation (MTT assay) was observed on gels that contained the highest amount of HA-o. The study shows that the beneficial EC response to HA oligomers and biocompatibility of HA is mostly unaltered by their chemical derivatization and crosslinking into a hydrogel. However, the study also demonstrates that the relatively high concentrations of DVS, necessary to create solid gels, compromises their biocompatibility. Moreover, the poor mechanics of even these heavily crosslinked gels, in the context of vascular implantation, necessitates the investigation of other, more appropriate crosslinking agents. Alternately, the outcomes of this study may be used to guide an approach based on chemical immobilization and controlled surface-presentation of both bioactive HA oligomers and more biocompatible HMW HAon synthetic or tissue engineered grafts already in use, without the use of a crosslinker, so that improved, predictable, and functional endothelialization can be achieved, and the need to create a mechanically compliant biomaterial for standalone use, circumvented. PMID:20186732

Fractionation and immunological characterization of allergens and allergoids of Prosopis juliflora pollen.

PubMed

Thakur, I S; Kamal; Mishra, S

1991-06-01

Allergoids of Prosopis juliflora pollen were prepared by formalinization of crude allergen and glycoprotein. Fractionation of crude allergen and allergoids on Sephadex G-100 resulted in separation of proteins of varying molecular size and a glycoprotein of 81 to 13 KD. Allergoids prepared from the glycoprotein fractionated into two proteins of approximately 200 KD and more than 200 KD. Crossed immunoelectrophoresis indicated 12 and gel diffusion test 3 precipitating antigens incrude allergen extract; by these tests allergoids depicted 8 and 3 precipitin bands, respectively. The precipitin analysis showed heterogeneity of allergenic determinants and also variation in cross-immunogenicity of the formalinized derivatives. The skin prick and radioallergosorbent tests depicted greater activity of fractionated crude allergens than the allergoids. The above tests suggest altered and concealed antigenic determinants as result of formalinization of P. juliflora pollen which, however, showed reduced allergenic activity relative to the native allergen.

NDUFS4 mutations cause Leigh syndrome with predominant brainstem involvement.

PubMed

Leshinsky-Silver, E; Lebre, Anne-Sophie; Minai, Limor; Saada, Ann; Steffann, Julie; Cohen, Sarit; Rötig, Agnes; Munnich, Arnold; Lev, Dorit; Lerman-Sagie, Tally

2009-07-01

Complex I deficiency is a frequent cause of Leigh syndrome. We describe a non-consanguineous Ashkenazi-Sephardic Jewish patient with Leigh syndrome due to complex I deficiency. The clinical and neuroradiological presentation showed predominant brainstem involvement. Blue native polyacrylamide gel electrophoresis analysis revealed an impaired assembly of complex I. The patient was found to be compound heterozygous of two mutations in the NDUFS4 gene: p.Asp119His (a novel mutation) and p.Lys154fs (recently described in an Ashkenazi Jewish family). These findings support the suggestion that the p.Lys154fs mutation in NDUFS4 should be evaluated in Ashkenazi Jewish patients presenting with early onset Leigh syndrome even before enzymatic studies. Our results further demonstrated that NDUFS4 presents a hotspot of mutations in the genetic apparatus of oxidative phosphorylation and the correct assembly of the subunit it encodes is essential for completion of the assembly of complex I.

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto.

PubMed

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

2010-12-01

Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27,724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a=74.3, b=49.9, c=56.3 Å, β=95.2°. Diffraction images were processed to a resolution of 1.74 Å with an Rmerge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase.

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto

PubMed Central

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

2010-01-01

Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27 724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a = 74.3, b = 49.9, c = 56.3 Å, β = 95.2°. Diffraction images were processed to a resolution of 1.74 Å with an R merge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase. PMID:21139221

Chemical modification of citrus pectin: Structural, physical and rheologial implications.

PubMed

Fracasso, Aline Francielle; Perussello, Camila Augusto; Carpiné, Danielle; Petkowicz, Carmen Lúcia de Oliveira; Haminiuk, Charles Windson Isidoro

2018-04-01

The present study aimed to investigate the physical, structural and rheological modifications caused by the chemical modification process of citrus pectin. Therefore, three commercial citrus pectins with different degree of esterification were chemically modified by sequential alkali and acidic hydrolytic process to produce modified citrus pectins (MCP) with special properties. The molar mass (M w ), degree of esterification (DE), monosaccharide composition, 13 C NMR spectra, homogeneity, morphology (SEM) and rheological behavior of both native and modified citrus pectins (MCP) were investigated. The chemical modification reduced the acid uronic content (up to 28.3%) and molar mass (up to 29.98%), however, showed little influence on the degree of esterification of native pectins. Modified citrus pectins presented higher amounts of neutral monosaccharides, mainly galactose, arabinose and rhamnose, typical of the Ramnogalacturonana-I (RG-I) region. Rheological tests indicated that the native and modified citrus pectins presented pseudoplastic behavior, however, the MCP samples were less viscous, compared to the native ones. Modified samples presented better dissolution in water and less strong gels, with good stability during oscillatory shearing at 25°C. This study aims to better understand the implications that chemical modifications may impose on the structure of citrus pectins. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Kapp, O.H.; Mainwaring, M.G.; Vinogradov, S.N.

A fraction of the extracellular hemoglobin of Lumbricus terrestris, obtained by gel filtration at neutral pH subsequent to dissociation either at pH 9.8 or at pH 4.0 or at pH 7.0 in 10 mM sodium phosphotungstate, consisting of the three subunits D1 (31 kDa), D2 (37 kDa) and T (50 kDa), produced two peaks when subjected to FPLC on a Superose 6 column at neutral pH. Peak I, eluting at a slightly greater volume than the native hemoglobin, consisted of reassociated hexagonal bilayer structures when examined by scanning transmission electron microscopy. The dimensions of the three reassociated hexagonal bilayer structuresmore » were 25 nm x 16 nm. Although the latter are smaller than the dimensions of the native hemoglobin, 30 nm x 20 nm, the diameter of the central cavity remained unchanged. Subtraction of the digitized and averaged images of the reassociated forms from those of the native hemoglobin suggested that the spatial localization of the fourth subunit, subunit M (16.7 kDa), was limited primarily to the periphery of the molecule.« less

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE PAGES

Foston, Marcus B.; Samuel, Reichel; He, Jian; ...

2016-01-19

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

A review of whole cell wall NMR by the direct-dissolution of biomass

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

Foston, Marcus B.; Samuel, Reichel; He, Jian

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

Limonoate dehydrogenase from Arthrobacter globiformis: the native enzyme and its N-terminal sequence.

PubMed

Suhayda, C G; Omura, M; Hasegawa, S

1995-09-01

Bitter limonoids in citrus juice lower the quality and value of commercial juices. Limonoate dehydrogenase converts the precursor of bitter limonin, limonoate A-ring lactone, to nonbitter 17-dehydrolimonoate A-ring lactone. This enzyme was isolated from Arthrobacter globiformis cells by a combination of ammonium sulfate fractionation, Cibacron Blue affinity chromatography and DEAE ion exchange HPLC. Using this protocol a 428-fold purification of the enzyme was obtained. Gel filtration HPLC indicated a M(r) of 118,000 for the native enzyme. SDS-PAGE indicated an individual subunit M(r) of 31,000. N-Terminal sequencing of the protein provided a sequence of the first 16 amino acid residues. Since LDH activity in citrus is very low, cloning the gene for this bacterial enzyme into citrus trees should enhance the natural debittering mechanism in citrus fruit.

Assay, Purification, and Partial Characterization of Choline Monooxygenase from Spinach.

PubMed Central

Burnet, M.; Lafontaine, P. J.; Hanson, A. D.

1995-01-01

The osmoprotectant glycine betaine is synthesized via the path-way choline -> betaine aldehyde -> glycine betaine. In spinach (Spinacia oleracea), the first step is catalyzed by choline monooxygenase (CMO), and the second is catalyzed by betaine aldehyde dehydrogenase. Because betaine aldehyde is unstable and not easily detected, we developed a coupled radiometric assay for CMO. [14C]Choline is used as substrate; NAD+ and betaine aldehyde dehydrogenase prepared from Escherichia coli are added to oxidize [14C]betaine aldehyde to [14C]glycine betaine, which is isolated by ion exchange. The assay was used in the purification of CMO from leaves of salinized spinach. The 10-step procedure included polyethylene glycol precipitation, polyethyleneimine precipitation, hydrophobic interaction, anion exchange on choline-Sepharose, dimethyldiethanolamine-Sepharose, and Mono Q, hydroxyapatite, gel filtration, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Following gel filtration, overall purification was about 600-fold and recovery of activity was 0.5%. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a polypeptide with a molecular mass of 45 kD. Taken with the value of 98 kD estimated for native CMO (R. Brouquisse, P. Weigel, D. Rhodes, C.F. Yocum, A.D. Hanson [1989] Plant Physiol 90: 322-329), this indicates that CMO is a homodimer. CMO preparations were red-brown, showed absorption maxima at 329 and 459 nm, and lost color upon dithionite addition, suggesting that CMO is an iron-sulfur protein. PMID:12228495

Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes.

PubMed

Jin, Ya; Yuan, Qi; Zhang, Jun; Manabe, Takashi; Tan, Wen

2015-09-01

Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an "overlap score," (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 "overlap factors," (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Prevalence, Level, and Types of Salmonella Isolated from North American In-Shell Pecans over Four Harvest Years.

PubMed

Brar, Pardeepinder K; Strawn, Laura K; Danyluk, Michelle D

2016-03-01

In-shell pecan samples (500 g) were collected over four harvest seasons (2010 to 2014) from seven pecan shelling facilities located in five U.S. states. Four varieties of pecans were analyzed: Mexican Improved, Native Seedlings, Southern Improved, and Western Improved. Pecan samples (100 g) were sent to a third party laboratory for initial Salmonella screening. When a sample was positive for Salmonella, the pathogen level was determined by the most-probable-number (MPN) method (25, 2.5, and 0.25 g). Two sample preparation strategies were used for the MPN analysis, and both strategies were combined for the reported MPN values. Forty-four (0.95%) of 4,641 in-shell pecan samples were positive for Salmonella during initial screening; prevalence by year was 0.47 to 1.4%. Prevalence was not significantly different between varieties: Mexican Improved, 1.2%; Native/Seedling, 0.99%; Southern Improved, 0.97%; and Western Improved, 0.75%. Salmonella was not isolated from 31 of 44 samples upon retesting during MPN analysis (<0.47 MPN/100 g). When Salmonella was detected, the levels were 0.47 to 39 MPN/100 g, with a mean of 2.4 MPN/100 g. Thirty-one Salmonella serotypes were obtained from 42 Salmonella-positive pecan samples; Enteritidis was the most common (12% of samples) followed by Javiana (9%) and Braenderup (7%). All Salmonella Enteritidis isolates were phage type 8. Pulsed-field gel electrophoresis analysis (XbaI) revealed within-serotype diversity, indicating introduction of contamination from a variety of sources. Most (64%) of the isolates were resistant to streptomycin or tetracycline, and 13% were resistant to three or more antibiotics. Salmonella prevalence and level on in-shell pecans is comparable to that on other nuts.

Purification and characterization of myrosinase from horseradish (Armoracia rusticana) roots.

PubMed

Li, Xian; Kushad, Mosbah M

2005-06-01

Myrosinase (beta-thioglucoside glucohydrolase; EC 3.2.3.147) from horseradish (Armoracia rusticana) roots was purified to homogeneity by ammonium sulfate fractionation, Q-sepharose, and concanavalin A sepharose affinity chromatography. The purified protein migrated as a single band with a mass of about 65 kDa on SDS-polyacrylamide gel electrophoresis. Using LC-MS/MS, this band was identified as myrosinase. Western blot analysis, using the anti-myrosinase monoclonal antibody 3D7, showed a single band of about 65 kDa for horseradish crude extract and for the purified myrosinase. The native molecular mass of the purified myrosinase was estimated, using gel filtration, to be about 130 kDa. Based on these data, it appeared that myrosinase from horseradish root consists of two subunits of similar molecular mass of about 65 kDa. The enzyme exhibited high activity at broad pH (pH 5.0-8.0) and temperature (37 and 45 degrees C). The purified enzyme remained stable at 4 degrees C for more than 1 year. Using sinigrin as a substrate, the Km and Vmax values for the purified enzyme were estimated to be 0.128 mM and 0.624 micromol min(-1), respectively. The enzyme was strongly activated by 0.5 mM ascorbic acid and was able to breakdown intact glucosinolates in a crude extract of broccoli.

A Sequence-Specific Nicking Endonuclease from Streptomyces: Purification, Physical and Catalytic Properties

PubMed Central

Somyoonsap, Peechapack; Kitpreechavanich, Vichein

2013-01-01

A sequence-specific nicking endonuclease from Streptomyces designated as DC13 was purified to near homogeneity. Starting with 30 grams of wet cells, the enzyme was purified by ammonium sulfate fractionation, DEAE cellulose, and phenyl-Sepharose chromatography. The purified protein had a specific activity 1000 units/mg and migrated on SDS-PAGE gel with an estimated molecular weight of 71 kDa. Determination of subunit composition by gel filtration chromatography indicated that the native enzyme is a monomer. When incubated with different DNA substrates including pBluescript II KS, pUC118, pET-15b, and pET-26b, the enzyme converted these supercoiled plasmids to a mixture of open circular and linear DNA products, with the open circular DNA as the major cleavage product. Analysis of the kinetic of DNA cleavage showed that the enzyme appeared to cleave super-coiled plasmid in two distinct steps: a rapid cleavage of super-coiled plasmid to an open circular DNA followed a much slower step to linear DNA. The DNA cleavage reaction of the enzyme required Mg2+ as a cofactor. Based on the monomeric nature of the enzyme, the kinetics of DNA cleavage exhibited by the enzyme, and cofactor requirement, it is suggested here that the purified enzyme is a sequence-specific nicking endonuclease that is similar to type IIS restriction endonuclease. PMID:25937959

Mucin gel assembly is controlled by a collective action of non-mucin proteins, disulfide bridges, Ca2+-mediated links, and hydrogen bonding.

PubMed

Meldrum, Oliver W; Yakubov, Gleb E; Bonilla, Mauricio R; Deshmukh, Omkar; McGuckin, Michael A; Gidley, Michael J

2018-04-11

Mucus is characterized by multiple levels of assembly at different length scales which result in a unique set of rheological (flow) and mechanical properties. These physical properties determine its biological function as a highly selective barrier for transport of water and nutrients, while blocking penetration of pathogens and foreign particles. Altered integrity of the mucus layer in the small intestine has been associated with a number of gastrointestinal tract pathologies such as Crohn's disease and cystic fibrosis. In this work, we uncover an intricate hierarchy of intestinal mucin (Muc2) assembly and show how complex rheological properties emerge from synergistic interactions between mucin glycoproteins, non-mucin proteins, and Ca 2+ . Using a novel method of mucus purification, we demonstrate the mechanism of assembly of Muc2 oligomers into viscoelastic microscale domains formed via hydrogen bonding and Ca 2+ -mediated links, which require the joint presence of Ca 2+ ions and non-mucin proteins. These microscale domains aggregate to form a heterogeneous yield stress gel-like fluid, the macroscopic rheological properties of which are virtually identical to that of native intestinal mucus. Through proteomic analysis, we short-list potential protein candidates implicated in mucin assembly, thus paving the way for identifying the molecules responsible for the physiologically critical biophysical properties of mucus.

Promoter mapping of the mouse Tcp-10bt gene in transgenic mice identifies essential male germ cell regulatory sequences.

PubMed

Ewulonu, U K; Snyder, L; Silver, L M; Schimenti, J C

1996-03-01

Transgenic mice were generated to localize essential promoter elements in the mouse testis-expressed Tcp-10 genes. These genes are expressed exclusively in male germ cells, and exhibit a diffuse range of transcriptional start sites, possibly due to the absence of a TATA box. A series of transgene constructs containing different amounts of 5' flanking DNA revealed that all sequences necessary for appropriate temporal and tissue-specific transcription of Tcp-10 reside between positions -1 to -973. All transgenic animals containing these sequences expressed a chimeric transgene at high levels, in a pattern that paralleled the endogenous genes. These experiments further defined a 227 bp fragment from -746 to -973 that was absolutely essential for expression. In a gel-shift assay, this 227-bp fragment bound nuclear protein from testis, but not other tissues, to yield two retarded bands. Sequence analysis of this fragment revealed a half-site for the AP-2 transcription factor recognition sequence. Gel shift assays using native or mutant oligonucleotides demonstrated that the putative AP-2 recognition sequence was essential for generating the retarded bands. Since the binding activity is testis-specific, but AP-2 expression is not exclusive to male germ cells, it is possible that transcription of Tcp-10 requires interaction between AP-2 and a germ cell-specific transcription factor.

Preparation of a highly concentrated, completely monomeric, active sarcoplasmic reticulum Ca2+-ATPase.

PubMed

Lüdi, H; Hasselbach, W

1985-11-21

Sarcoplasmic reticulum vesicles from fast skeletal muscle were partially delipidated with sodium cholate at high ionic strength and sedimented in a discontinuous sucrose gradient. Phospholipid content was reduced from 0.777 mumol/mg protein to 0.242 mumol/mg protein. As judged from gel electrophoresis and high pressure liquid gel chromatography, accessory proteins were removed during centrifugation and the Ca2+-ATPase was obtained in an almost pure form. Addition of myristoylglycerophosphocholine (1 mg/mg protein) reactivates ATPase and dinitrophenylphosphatase activity to the same degree obtained with native vesicles. Using the analytical ultracentrifuge it could be demonstrated that the reactivated Ca2+-ATPase was present exclusively in a monomeric state. These results were obtained at high and low ionic strength and up to a protein concentration of 10 mg/ml. Therefore this preparation should be very useful to investigate differences between oligomeric and monomeric Ca2+-ATPase.

Multiple forms of endopeptidase activity from jojoba seeds.

PubMed

Wolf, M J; Storey, R D

1990-01-01

The cotyledons of 27 day post-germination jojoba seedlings (Simmondsia chinensis) contained five distinct endopeptidase activities separable by DEAE Bio-Gel and CM-cellulose ion exchange chromatography. The endopeptidases were purified 108- to 266-fold and their individuality was confirmed by activity-specific assays in native acrylamide gels along with differences in their Mr and catalytic properties. The five endopeptidases, which showed activity on model substrates and protein, were named EP Ia, EP Ib, EP II, EP III and EP IV. EP Ia was a serine proteinase with a pH optimum of ca 8 and Mr of 58,000. EP Ib, II and III were discrete cysteine proteinases showing pH optima of ca 6.8, 6.0 and 5.4 and Mr of 41,000, 47,000 and 35,000 respectively. EP IV was an aspartic acid proteinase with a ca pH optimum of 3.5 and Mr of 33,000.

Flavourzyme, an Enzyme Preparation with Industrial Relevance: Automated Nine-Step Purification and Partial Characterization of Eight Enzymes.

PubMed

Merz, Michael; Eisele, Thomas; Berends, Pieter; Appel, Daniel; Rabe, Swen; Blank, Imre; Stressler, Timo; Fischer, Lutz

2015-06-17

Flavourzyme is sold as a peptidase preparation from Aspergillus oryzae. The enzyme preparation is widely and diversely used for protein hydrolysis in industrial and research applications. However, detailed information about the composition of this mixture is still missing due to the complexity. The present study identified eight key enzymes by mass spectrometry and partially by activity staining on native polyacrylamide gels or gel zymography. The eight enzymes identified were two aminopeptidases, two dipeptidyl peptidases, three endopeptidases, and one α-amylase from the A. oryzae strain ATCC 42149/RIB 40 (yellow koji mold). Various specific marker substrates for these Flavourzyme enzymes were ascertained. An automated, time-saving nine-step protocol for the purification of all eight enzymes within 7 h was designed. Finally, the purified Flavourzyme enzymes were biochemically characterized with regard to pH and temperature profiles and molecular sizes.

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

PubMed Central

Hellman, Lance M.; Fried, Michael G.

2009-01-01

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

Comparison of micronized tretinoin gel 0.05% and tretinoin gel microsphere 0.1% in young adolescents with acne: a post hoc analysis of efficacy and tolerability data.

PubMed

Lucky, Anne W; Sugarman, Jeffrey

2011-06-01

Acne vulgaris is common in young adolescents. Retinoids are widely used but may be associated with poor tolerability. This post hoc analysis of 483 participants aged 10 to 14 years with mild to moderate acne compared efficacy and tolerability of once-daily treatment with micronized tretinoin gel 0.05%, tretinoin gel microsphere 0.1%, and vehicle over 12 weeks. In study 1, inflammatory and noninflammatory lesion reduction and treatment success was comparable between tretinoin gel 0.05% and tretinoin gel microsphere 0.1%. Inflammatory (46.3%) and noninflammatory (45.7%) lesion reductions with tretinoin gel 0.05% were significantly greater than vehicle (37.1% and 27.9%, respectively) (both P<.001). In study 2, inflammatory and noninflammatory lesion reductions and treatment success with tretinoin gel 0.05% (30.6%, 39.1%, and 19%, respectively) were significantly greater than vehicle (10.9%, 16.9% [both P<.001], and 4% [P=.008], respectively). Tretinoin gel 0.05% was significantly better tolerated than tretinoin gel microsphere 0.1% (P<.001); the majority of adverse events (AEs) were mild, occurring in the first 2 weeks. Fourteen percent of participants reported dry skin, 8% skin burning sensation, 5% erythema, and 5% dermatitis exfoliative with tretinoin gel 0.05% compared with 32%, 11%, 23%, and 23%, respectively, with tretinoin gel microsphere 0.1% (all P<.001, except skin burning sensation). In this secondary analysis of acne in young adolescents aged 10 to 14 years, micronized tretinoin gel 0.05% provided a comparable lesion reduction and treatment success versus tretinoin gel microsphere 0.1%, with a better cutaneous tolerability profile.

Purification and characterization of caffeine synthase from tea leaves.

PubMed

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

1999-06-01

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

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

NASA Astrophysics Data System (ADS)

Wen, Edward Z.; Luo, Ray

2004-08-01

The denatured state of a miniprotein BBA1 is studied under the native condition with the AMBER/Poisson-Boltzmann energy model and with the self-guided enhanced sampling technique. Forty independent trajectories are collected to sample the highly diversified denatured structures. Our simulation data show that the denatured BBA1 contains high percentage of native helix and native turn, but low percentage of native hairpin. Conditional population analysis indicates that the native helix formation and the native hairpin formation are not cooperative in the denatured state. Side-chain analysis shows that the native hydrophobic contacts are more preferred than the non-native hydrophobic contacts in the denatured BBA1. In contrast, the salt-bridge contacts are more or less nonspecific even if their populations are higher than those of hydrophobic contacts. Analysis of the trajectories shows that the native helix mostly initiates near the N terminus and propagates to the C terminus, and mostly forms from 310-helix/turn to α helix. The same analysis shows that the native turn is important but not necessary in its formation in the denatured BBA1. In addition, the formations of the two strands in the native hairpin are rather asymmetric, demonstrating the likely influence of the protein environment. Energetic analysis shows that the native helix formation is largely driven by electrostatic interactions in denatured BBA1. Further, the native helix formation is associated with the breakup of non-native salt-bridge contacts and the accumulation of native salt-bridge contacts. However, the native hydrophobic contacts only show a small increase upon the native helix formation while the non-native hydrophobic contacts stay essentially the same, different from the evolution of hydrophobic contacts observed in an isolated helix folding.

Monoclonal antibodies against the native urease of Helicobacter pylori: synergistic inhibition of urease activity by monoclonal antibody combinations.

PubMed Central

Nagata, K; Mizuta, T; Tonokatu, Y; Fukuda, Y; Okamura, H; Hayashi, T; Shimoyama, T; Tamura, T

1992-01-01

Monoclonal antibodies (MAbs) against the native urease of Helicobacter pylori NCTC 11637 were found to clearly inhibit the urease activity. Interestingly, synergistic inhibition by two MAbs recognizing different subunits was also observed. Ten MAbs were produced and classified as two isotypes of the immunoglobulin G (IgG) subclass, IgG1, and IgG2a. Western blot (immunoblot) analysis using sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that five MAbs recognized the large subunit and the other five recognized the small subunit of the urease. Among the MAbs, L2 and S2, which recognized the large and the small subunits, respectively, were also able to inhibit the urease activity of clinical isolates from H. pylori-infected patients. The combination of L2 and S2 led to augmented synergistic inhibition. L2, but not S2, could also inhibit the urease activity from Helicobacter mustelae; enzyme-linked immunosorbent assay and Western blot analysis showed that L2 cross-reacted with this urease. These results suggested that the epitope recognized by L2 had a structure common to both Helicobacter species and may be involved in the active site of the urease. In contrast to the MAbs, a polyclonal antibody in sera from mice immunized with H. pylori urease did not have the ability to inhibit H. pylori urease activity. However, the polyclonal antibody retained the ability to abolish the inhibitory action of these MAbs. Moreover, other MAbs which could not inhibit H. pylori urease activity also abolished the inhibitory action. Images PMID:1383158

Bifunctional activity of deoxyhypusine synthase/hydroxylase from Trichomonas vaginalis.

PubMed

Quintas-Granados, Laura Itzel; Carvajal Gamez, Bertha Isabel; Villalpando, Jose Luis; Ortega-Lopez, Jaime; Arroyo, Rossana; Azuara-Liceaga, Elisa; Álvarez-Sánchez, María Elizbeth

2016-04-01

The Trichomonas vaginalis genome analysis suggested the presence of a putative deoxyhypusine synthase (TvDHS) that catalyzes the posttranslational modification of eIF-5A. Herein, we expressed and purified the recombinant TvDHS (rTvDHS) protein (43 kDa) and the recombinant TveIF-5A (rTveIF-5A) precursor protein (46 kDa). A 41 kDa band of the native TvDHS was recognized by western blot analysis in T. vaginalis total protein extract by a mouse polyclonal anti-rTvDHS antibody. The enzymatic activity of rTvDHS was determined by in vitro rTveIF-5A precursor modification. The modification reaction was performed by using ((3)H)-spermidine, and the biochemical analysis showed that rTvDHS exhibited Km value of 0.6 μM. The rTvDHS activity was inhibited by the spermidine analog, N″-guanyl-1,7-diamino-heptane (GC7). Native gel electrophoresis analysis showed two bands corresponding to an rTvDHS-rTveIF-5A complex and an intermediate form of rTveIF-5A. The two forms were subsequently separated by ion exchange chromatography to identify the hypusine residue by MS/MS analysis. Moreover, mutations in TvDHS showed that the putative HE motif present in this enzyme is involved in the hydroxylation of TveIF-5A. We observed that only hypusine-containing TveIF-5A was bound to an RNA hairpin ERE structure from the cox-2 gene, which contains the AAAUGUCACAC consensus sequence. Interestingly, 2DE-WB assays, using parasites that were grown in DAB-culture conditions and transferred to exogenous putrescine, showed the new isoform of TveIF-5A. In summary, our results indicate that T. vaginalis contains an active TvDHS capable of modifying the precursor TveIF-5A protein, which subsequently exhibits RNA binding activity. Copyright © 2015. Published by Elsevier B.V.

Tetrameric subunit structure of the native brain inwardly rectifying potassium channel Kir 2.2.

PubMed

Raab-Graham, K F; Vandenberg, C A

1998-07-31

Strongly inwardly rectifying potassium channels of the Kir 2 subfamily (IRK1, IRK2, and IRK3) are involved in maintenance and modulation of cell excitability in brain and heart. Electrophysiological studies of channels expressed in heterologous systems have suggested that the pore-conducting pathway contains four subunits. However, inferences from electrophysiological studies have not been tested on native channels and do not address the possibility of nonconducting auxiliary subunits. Here, we investigate the subunit stoichiometry of endogenous inwardly rectifying potassium channel Kir 2.2 (IRK2) from rat brain. Using chemical cross-linking, immunoprecipitiation, and velocity sedimentation, we report physical evidence demonstrating the tetrameric organization of the native channel. Kir 2.2 was sequentially cross-linked to produce bands on SDS-polyacrylamide gel electrophoresis corresponding in size to monomer, dimer, trimer, and three forms of tetramer. Fully cross-linked channel was present as a single band of tetrameric size. Immunoprecipitation of biotinylated membranes revealed a single band corresponding to Kir 2.2, suggesting that the channel is composed of a single type of subunit. Hydrodynamic properties of 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonic acid-solubilized channel were used to calculate the molecular mass of the channel. Velocity sedimentation in H2O or D2O gave a sharp peak with a sedimentation coefficient of 17.3 S. Gel filtration yielded a Stokes radius of 5.92 nm. These data indicate a multisubunit protein with a molecular mass of 193 kDa, calculated to contain 3.98 subunits. Together, these results demonstrate that Kir 2.2 channels are formed by the homotetrameric association of Kir 2.2 subunits and do not contain tightly associated auxiliary subunits. These studies suggest that Kir 2.2 channels differ in structure from related heterooctomeric ATP-sensitive K channels and heterotetrameric G-protein-regulated inward rectifier K channels.

GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images.

PubMed

Young, Nelson; Chang, Zhan; Wishart, David S

2004-04-12

GelScape is a web-based tool that permits facile, interactive annotation, comparison, manipulation and storage of protein gel images. It uses Java applet-servlet technology to allow rapid, remote image handling and image processing in a platform-independent manner. It supports many of the features found in commercial, stand-alone gel analysis software including spot annotation, spot integration, gel warping, image resizing, HTML image mapping, image overlaying as well as the storage of gel image and gel annotation data in compliance with Federated Gel Database requirements.

Alteration of plasma membrane-bound redox systems of iron deficient pea roots by chitosan.

PubMed

Meisrimler, Claudia-Nicole; Planchon, Sebastien; Renaut, Jenny; Sergeant, Kjell; Lüthje, Sabine

2011-08-12

Iron is essential for all living organisms and plays a crucial role in pathogenicity. This study presents the first proteome analysis of plasma membranes isolated from pea roots. Protein profiles of four different samples (+Fe, +Fe/Chitosan, -Fe, and -Fe/Chitosan) were compared by native IEF-PAGE combined with in-gel activity stains and DIGE. Using DIGE, 89 proteins of interest were detected in plasma membrane fractions. Data revealed a differential abundance of several spots in all samples investigated. In comparison to the control and -FeCh the abundance of six protein spots increased whereas 56 spots decreased in +FeCh. Altered protein spots were analyzed by MALDI-TOF-TOF mass spectrometry. Besides stress-related proteins, transport proteins and redox enzymes were identified. Activity stains after native PAGE and spectrophotometric measurements demonstrated induction of a ferric-chelate reductase (-Fe) and a putative respiratory burst oxidase homolog (-FeCh). However, the activity of the ferric-chelate reductase decreased in -Fe plants after elicitor treatment. The activity of plasma membrane-bound class III peroxidases increased after elicitor treatment and decreased under iron-deficiency, whereas activity of quinone reductases decreased mostly after elicitor treatment. Possible functions of proteins identified and reasons for a weakened pathogen response of iron-deficient plants were discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

In vitro fermentative capacity of swine large intestine: comparison between native Lantang and commercial Duroc breeds.

PubMed

Cheng, Peng Hui; Liang, Juan Boo; Wu, Yin Bao; Wang, Yan; Tufarelli, Vincenzo; Laudadio, Vito; Liao, Xin Di

2017-08-01

Native Lantang and commercial Duroc pigs were used as animal models to evaluate the differences existing in dietary fiber utilization ability between breeds. Animals were fed the same diet from weaning (4 weeks) to 4 months of age. Neutral detergent fiber (NDF) from wheat bran (as substrate) and fecal samples from the two breeds (as inoculum) were used in an in vitro gas production trial. Results showed that cumulative and maximum gas productions were higher in inocula from Lantang than those from the Duroc breed (P < 0.05). The degradation capacity of NDF for microbiome from Lantang fecal samples were significantly higher compared to Duroc (P < 0.01). The total quantity of short-chain fatty acids and its constituents from the fermentation liquors were different between breeds, suggesting that the dynamic characteristics of fermentation differed between the two breeds. The PCR denaturing gradient gel electrophoresis fingerprint and cluster analysis demonstrated that microbial communities of the two breeds were separated into two clusters and the bacterial community structure of large intestine among the two breed of pigs was different. Our results concluded that Lantang had higher dietary fiber degradation capacity than Duroc pigs, and the higher degradation capacity for the former breed was due to differences in the inherent microbial community in their respective large intestines. © 2016 Japanese Society of Animal Science.

Biochemical characterisation of urease from urease-positive thermophilic campylobacter (UPTC).

PubMed

Tazumi, A; Nakajima, T; Sekizuka, A; Arikawa, K; Nakanishi, S; Hayashi, K; Tasaki, E; Moore, J E; Millar, B C; Matsuda, M

2012-01-01

This study aims to characterise biochemically urease from an atypical Campylobacter lari, namely urease-positive thermophilic Campylobacter (UPTC). Urease was purified from cells of a Japanese UPTC isolate (CF89-12) using phenyl-Sepharose chromatography. Two protein components (estimates molecular masses 24 kDa and 61 kDa) were obtained that appeared to be structural proteins of urease (subunits A and B), and these were fractionated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (PAGE). The native molecular weight for the final purified UPTC urease was estimated to be approximately 186,000 Da which is close to the calculated molecular weight (182,738 Da) based on all six open reading frames of UPTC CF89-12 urease genes (ureA, B, E, F, G and H), as described previously. Moreover, an active band was observed on phenol red staining after a nondenaturing native PAGE of the crude extract from the UPTC cells. In addition, the purified urease of UPTC CF8912 showed enzyme activity over a broad pH range (pH 6-10), with maximal activity at pH 8.0. The urease was also stable against heat treatment, with almost no loss of enzyme activity seen following 60-min incubation at temperatures of 20-60 degrees C. Urease subunits A and B were identified immunologically by Western blot analysis with rabbit anti-urease alpha (A) and beta (B) raised against Helicobacter pylori.

Isolation, electron microscopic imaging, and 3-D visualization of native cardiac thin myofilaments.

PubMed

Spiess, M; Steinmetz, M O; Mandinova, A; Wolpensinger, B; Aebi, U; Atar, D

1999-06-15

An increasing number of cardiac diseases are currently pinpointed to reside at the level of the thin myofilaments (e.g., cardiomyopathies, reperfusion injury). Hence the aim of our study was to develop a new method for the isolation of mammalian thin myofilaments suitable for subsequent high-resolution electron microscopic imaging. Native cardiac thin myofilaments were extracted from glycerinated porcine myocardial tissue in the presence of protease inhibitors. Separation of thick and thin myofilaments was achieved by addition of ATP and several centrifugation steps. Negative staining and subsequent conventional and scanning transmission electron microscopy (STEM) of thin myofilaments permitted visualization of molecular details; unlike conventional preparations of thin myofilaments, our method reveals the F-actin moiety and allows direct recognition of thin myofilament-associated porcine cardiac troponin complexes. They appear as "bulges" at regular intervals of approximately 36 nm along the actin filaments. Protein analysis using SDS-polyacrylamide gel electrophoresis revealed that only approximately 20% troponin I was lost during the isolation procedure. In a further step, 3-D helical reconstructions were calculated using STEM dark-field images. These 3-D reconstructions will allow further characterization of molecular details, and they will be useful for directly visualizing molecular alterations related to diseased cardiac thin myofilaments (e.g., reperfusion injury, alterations of Ca2+-mediated tropomyosin switch). Copyright 1999 Academic Press.

Life history traits and the activity of antioxidative enzymes in Lymantria dispar L. (lepidoptera, lymantriidae) larvae exposed to benzo[a]pyrene.

PubMed

Ilijin, Larisa; Mrdaković, Marija; Todorović, Dajana; Vlahović, Milena; Gavrilović, Anja; Mrkonja, Aleksandra; Perić-Mataruga, Vesna

2015-11-01

Increased presence of benzo[a]pyrene in the environment underlines the need for development of sensitive biomarkers for monitoring. Antioxidative enzymes could be used as early-warning signals because of their sensitivity and applicability. The activity of 2 antioxidative enzymes, superoxide dismutase (SOD) and catalase (CAT), were measured in midgut tissues of fifth instar Lymantria dispar larvae exposed to different concentrations of benzo[a]pyrene: 2 ng, 10 ng, 20 ng, 100 ng, 200 ng, and 2000 ng benzo[a]pyrene/g dry food weight. Larval development, larval mass, and relative growth rate were also monitored. The authors detected prolonged larval development, as well as reduced larval mass and relative growth rate in larvae exposed to all benzo[a]pyrene concentrations. The L. dispar midgut SOD activity was significantly increased, and 2 SOD isoforms were detected on native polyacrylamide gel electrophoresis in larvae fed on artificial diet supplemented with benzo[a]pyrene. In contrast, the control group had only 1 isoform. Catalase activity was significantly increased in all benzo[a]pyrene-treated larvae. Native gel electrophoresis showed that a switch in active CAT isoforms occurred after benzo[a]pyrene treatment. Thus, SOD and CAT in polyphagous herbivorous L. dispar larvae are very sensitive to low concentrations of benzo[a]pyrene. Therefore, they could be used as biomarkers for exposure and effects of this toxic polycyclic aromatic hydrocarbon. © 2015 SETAC.

Expression, purification and biochemical characterization of a single-stranded DNA binding protein from Herbaspirillum seropedicae.

PubMed

Vernal, Javier; Serpa, Viviane I; Tavares, Carolina; Souza, Emanuel M; Pedrosa, Fábio O; Terenzi, Hernán

2007-05-01

An open reading frame encoding a protein similar in size and sequence to the Escherichia coli single-stranded DNA binding protein (SSB protein) was identified in the Herbaspirillum seropedicae genome. This open reading frame was cloned into the expression plasmid pET14b. The SSB protein from H. seropedicae, named Hs_SSB, was overexpressed in E. coli strain BL21(DE3) and purified to homogeneity. Mass spectrometry data confirmed the identity of this protein. The apparent molecular mass of the native Hs_SSB was estimated by gel filtration, suggesting that the native protein is a tetramer made up of four similar subunits. The purified protein binds to single-stranded DNA (ssDNA) in a similar manner to other SSB proteins. The production of this recombinant protein in good yield opens up the possibility of obtaining its 3D-structure and will help further investigations into DNA metabolism.

Purification and characterization of a trypsin inhibitor from the seeds of Artocarpus heterophyllus Lam.

PubMed

Lyu, Junchen; Liu, Yuan; An, Tianchen; Liu, Yujun; Wang, Manchuriga; Song, Yanting; Zheng, Feifei; Wu, Dan; Zhang, Yingxia; Deng, Shiming

2015-05-01

A proteinaceous inhibitor against trypsin was isolated from the seeds of Artocarpus heterophyllus Lam. by successive ammonium sulfate precipitation, ion-exchange, and gel-filtration chromatography. The trypsin inhibitor, named as AHLTI (A. heterophyllus Lam. trypsin inhibitor), consisted of a single polypeptide chain with a molecular weight of 28.5 kDa, which was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel-filtration chromatography. The N-terminal sequence of AHLTI was DEPPSELDAS, which showed no similarity to other known trypsin inhibitor sequence. AHLTI completely inhibited bovine trypsin at a molar ratio of 1:2 (AHLTI:trypsin) analyzed by native polyacrylamide gel electrophoresis, inhibition activity assay, and gel-filtration chromatography. Moreover, kinetic enzymatic studies were carried out to understand the inhibition mechanism of AHLTI against trypsin. Results showed that AHLTI was a competitive inhibitor with an equilibrium dissociation constant (Ki) of 3.7 × 10(-8) M. However, AHLTI showed weak inhibitory activity toward chymotrypsin and elastase. AHLTI was stable over a broad range of pH 4-8 and temperature 20-80°C. The reduction agent, dithiothreitol, had no obvious effect on AHLTI. The trypsin inhibition assays of AHLTI toward digestive enzymes from insect pest guts in vitro demonstrated that AHLTI was effective against enzymes from Locusta migratoria manilensis (Meyen). These results suggested that AHLTI might be a novel trypsin inhibitor from A. heterophyllus Lam. belonging to Kunitz family, and play an important role in protecting from insect pest. © The Author 2015. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

The cassava (Manihot esculenta Crantz) root proteome: protein identification and differential expression.

PubMed

Sheffield, Jeanne; Taylor, Nigel; Fauquet, Claude; Chen, Sixue

2006-03-01

Using high-resolution 2-DE, we resolved proteins extracted from fibrous and tuberous root tissues of 3-month-old cassava plants. Gel image analysis revealed an average of 1467 electrophoretically resolved spots on the fibrous gels and 1595 spots on the tuberous gels in pH 3-10 range. Protein spots from both sets of gels were digested with trypsin. The digests were subjected to nanoelectrospray quadrupole TOF tandem mass analysis. Currently, we have obtained 299 protein identifications for 292 gel spots corresponding to 237 proteins. The proteins span various functional categories from energy, primary and secondary metabolism, disease and defense, destination and storage, transport, signal transduction, protein synthesis, cell structure, and transcription to cell growth and division. Gel image analysis has shown unique, as well as up- and down-regulated proteins, present in the tuberous and the fibrous tissues. Quantitative and qualitative analysis of the cassava root proteome is an important step towards further characterization of differentially expressed proteins and the elucidation of the mechanisms underlying the development and biological functions of the two types of roots.

Polymorphism of Trp64Arg in beta3-adrenergic receptor gene among Bolivian people in rural areas at high and low altitudes.

PubMed

Karasaki, Yuji; Kashiwazaki, Hiroshi

2004-01-01

To investigate whether population differences in food and/or lifestyle could affect the distribution frequencies of polymorphism in the gene for beta3-adrenergic receptor (beta3-AR), the frequency of Trp64Arg polymorphism was studied among Bolivian people living in rural areas of high (about 4000 m above sea level) and low (about 300 m above sea level) altitudes. Genomic DNA samples of Bolivian subjects (n=508) were amplified by polymerase chain reaction (PCR) for part of the beta3-AR gene. The amplified PCR products were digested with restriction enzyme NciI and analysed by agarose gel electrophoresis. We found no significant difference in the frequency of Arg allele in the beta3-AR gene between 331 native low-altitude Bolivian subjects (18.1%) and 177 native high-altitude Bolivian subjects (17.5%). Body mass index was not associated with Trp64Arg polymorphism among native Bolivian adults. The frequency of this allele in the complete Bolivian population (18%) was lower than that reported in Pima Indians (32%), is comparable to the Japanese (19%) and is higher than several ethnic groups, including Finns (12%) and French (4%). Our data indicate that the altitude-related lifestyle of a population has had little influence on the frequency of Trp64Arg polymorphism and obesity in Bolivian natives.

Starch-based xerogels: Effect of acetylation on Physicochemical and rheological properties.

PubMed

Kemas, Chinwe U; Ngwuluka, Ndidi C; Ochekpe, Nelson A; Nep, Elijah I

2017-05-01

This study was aimed at evaluating the physicochemical and rheological properties of starch-based xerogels. The starch from the shoots of Borassus aethiopium was physically modified by xerogelization, and chemically by acetylation, and combination of acetylation and xerogelization. The solubility, swelling and syneresis of the starches were determined by gravimetric techniques. Evaluation of the native starch and derivatives was done using microscopy, Fourier transform infra-red (FTIR), x-ray diffractometry (XRD), and 1 H NMR spectroscopy. Rheological evaluation was done on 10%w/v dispersions using a Bohlin Gemini rheometer (fitted with a 55mm and 2° cone and plate geometry with gap of 70). The diffractograms displayed three peaks, centered on 2θ=15.3, 17.2 and 23.1° for the native and the starch acetate while the xerogel and the starch acetate xerogel were amorphous. The 1 H NMR and FTIR confirmed the presence of acetyl groups at about 2.05ppm and 1720cm -1 , respectively. Acetylation of the native starch resulted in improvement of solubility. The starch acetate-xerogel sample formed viscoelastic gels without the need for heating. Acetylation and/or xerogelization of the native starch inhibited syneresis. Starch acetate-xerogels, may find application as stabilizer or suspending agent in liquid food and pharmaceutical formulations. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization of a Cadmium-Binding Complex of Cabbage Leaves 1

PubMed Central

Wagner, George J.

1984-01-01

The chemical nature of a principal, inducible cadmium-binding complex which accumulates in cabbage leaves (Wagner and Trotter 1982 Plant Physiol 69: 804-809) was studied and compared with that of animal metallothionein and copper-binding proteins isolated from various organisms. The apparent molecular weight of native cabbage complex and carboxymethylated ligand of the complex under native conditions as determined by gel filtration was about 10,000 daltons. Under denaturing conditions their apparent molecular weights were about 2000 daltons. Ligand of native complex contained 37, 28, and 9 residue per cent of glutamic acid-glutamine, cysteine, and glycine, respectively, and low aromatic residue, serine and lysine content. The high acidic and low hydrophobic residue content explain the behavior of complex on electrophoresis in the presence and absence of sodium dodecyl sulfate. Its isoelectric point was below 4.0 and it bound 4 to 6 moles cadmium per mole ligand in what appear to be cadmium-mercaptide chromophores. The complex was found to be heat stable, relatively protease insensitive, and lacking in disulfide bonds. Attempts to determine the primary sequence of reduced native complex and carboxymethylated, cleaved ligand using the Edman degradation procedure were unsuccessful. An electrophoretic procedure is described for preparative isolation of purified complex and a method is described for monitoring ligand of complex as its fluorescent dibromobimane adduct. Images Fig. 1 Fig. 3 PMID:16663927

New GlcNAc/GalNAc-specific lectin from the ascidian Didemnum ternatanum.

PubMed

Molchanova, Valentina; Chikalovets, Irina; Li, Wei; Kobelev, Stanislav; Kozyrevskaya, Svetlana; Bogdanovich, Raisa; Howard, Eric; Belogortseva, Natalia

2005-05-25

Previously we isolated GlcNAc-specific lectin (DTL) from the ascidian Didemnum ternatanum by affinity chromatography on cross-linked ovalbumin. Here we report the purification and characterization of new D-GlcNAc/D-GalNAc-specific lectin DTL-A from the same ascidian. This lectin was isolated from non-bound cross-linked ovalbumin fraction and further was purified by gel filtration on Sepharose CL-4B, affinity chromatography on GlcNAc-agarose and gel filtration on Superdex 200. SDS-polyacrylamide gel electrophoresis and gel filtration of purified lectin on Sepharose CL-4B indicates that it exists as large aggregates in the native state. Investigations of the carbohydrate specificity of DTL-A by enzyme-linked lectin assay suggest the multi-specificity of this lectin. DTL-A binds BSM, asialo-BSM as well as heparin and dextran sulfate. The binding of DTL-A to BSM was inhibited by monosaccharides D-GlcNAc and D-GalNAc, their alpha- but not beta-anomers. Among polysaccharides and glycoconjugates, DTL-A binding to BSM was effectively inhibited by BSM, asialo-BSM, pronase-treated BSM and synthetic alpha-D-GalNAc-PAA. Fetuin and asialofetuin showed a much lower inhibitory potency, heparin and dextran sulfate were noninhibitory. On the other hand, DTL-A binding to heparin was effectively inhibited by dextran sulfate, fucoidan, whereas BSM showed insignificantly inhibitory effect. DTL-A binding to heparin was not inhibited by D-GlcNAc and D-GalNAc.

Soft nanocomposites of gelatin and poly(3-hydroxybutyrate) nanoparticles for dual drug release.

PubMed

Bini, Rafael A; Silva, Mônica F; Varanda, Laudemir C; da Silva, Marcelo A; Dreiss, Cécile A

2017-09-01

We developed a nanocomposite gel composed of gelatin and poly(3-hydroxybutyrate) polymeric nanoparticles (PNP) to be used as an injectable gel for the contemporaneous, dual sustained release of bioactive molecules. The hydrogel matrix was formed by a very simple process, using either the physical gelation of gelatin or the natural enzyme transglutaminase to covalently cross-link the gelatin chains in the presence of embedded PNP. Oscillatory rheological measurements showed that the addition of the PNP induced an increase in the storage modulus compared to pure gelatin gels, for both physical and chemical gels. Micrographs from scanning electron microscopy revealed that the presence of PNP disrupted the native structure of the gelatin chains in the hydrogel matrix. Dual drug encapsulation was achieved with curcumin (CM) in the PNP and naproxen sodium(NS) in the gelatin matrix. In vitro release studies showed that the hydrogel matrix acts both as a physical and chemical barrier, delaying the diffusion of the drugs. An initial burst release was observed in the first hours of the measurement, and around 90% was released on the third day for naproxen sodium. In free PNP, 82% of curcumin was relased after four days, while when PNP were embedded in the gelatin matrix only 40% was released over the same time period. Overall, these simple, sustainable soft nanocomposites show potential as an injectable co-sustained drug release system. Copyright © 2017 Elsevier B.V. All rights reserved.

Anatomically realistic ultrasound phantoms using gel wax with 3D printed moulds

NASA Astrophysics Data System (ADS)

Maneas, Efthymios; Xia, Wenfeng; Nikitichev, Daniil I.; Daher, Batol; Manimaran, Maniragav; Wong, Rui Yen J.; Chang, Chia-Wei; Rahmani, Benyamin; Capelli, Claudio; Schievano, Silvia; Burriesci, Gaetano; Ourselin, Sebastien; David, Anna L.; Finlay, Malcolm C.; West, Simeon J.; Vercauteren, Tom; Desjardins, Adrien E.

2018-01-01

Here we describe methods for creating tissue-mimicking ultrasound phantoms based on patient anatomy using a soft material called gel wax. To recreate acoustically realistic tissue properties, two additives to gel wax were considered: paraffin wax to increase acoustic attenuation, and solid glass spheres to increase backscattering. The frequency dependence of ultrasound attenuation was well described with a power law over the measured range of 3-10 MHz. With the addition of paraffin wax in concentrations of 0 to 8 w/w%, attenuation varied from 0.72 to 2.91 dB cm-1 at 3 MHz and from 6.84 to 26.63 dB cm-1 at 10 MHz. With solid glass sphere concentrations in the range of 0.025-0.9 w/w%, acoustic backscattering consistent with a wide range of ultrasonic appearances was achieved. Native gel wax maintained its integrity during compressive deformations up to 60%; its Young’s modulus was 17.4  ±  1.4 kPa. The gel wax with additives was shaped by melting and pouring it into 3D printed moulds. Three different phantoms were constructed: a nerve and vessel phantom for peripheral nerve blocks, a heart atrium phantom, and a placental phantom for minimally-invasive fetal interventions. In the first, nerves and vessels were represented as hyperechoic and hypoechoic tubular structures, respectively, in a homogeneous background. The second phantom comprised atria derived from an MRI scan of a patient with an intervening septum and adjoining vena cavae. The third comprised the chorionic surface of a placenta with superficial fetal vessels derived from an image of a post-partum human placenta. Gel wax is a material with widely tuneable ultrasound properties and mechanical characteristics that are well suited for creating patient-specific ultrasound phantoms in several clinical disciplines.

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

PubMed

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

2017-08-01

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

Thermodynamic analysis of sol-gel transition of gelatin in terms of water activity in various solutions.

PubMed

Miyawaki, Osato; Omote, Chiaki; Matsuhira, Keiko

2015-12-01

Sol-gel transition of gelatin was analyzed as a multisite stoichiometric reaction of a gelatin molecule with water and solute molecules. The equilibrium sol-gel transition temperature, Tt , was estimated from the average of gelation and melting temperature measured by differential scanning calorimetry. From Tt and the melting enthalpy, ΔHsol , the equilibrium sol-to-gel ratio was estimated by the van't Hoff equation. The reciprocal form of the Wyman-Tanford equation, which describes the sol-to-gel ratio as a function of water activity, was successfully applied to obtain a good linear relationship. From this analysis, the role of water activity on the sol-gel transition of gelatin was clearly explained and the contributions of hydration and solute binding to gelatin molecules were separately discussed in sol-gel transition. The general solution for the free energy for gel-stabilization in various solutions was obtained as a simple function of solute concentration. © 2015 Wiley Periodicals, Inc.

Alpha-2-Macroglobulin Is Acutely Sensitive to Freezing and Lyophilization: Implications for Structural and Functional Studies

PubMed Central

Wyatt, Amy R.; Kumita, Janet R.; Farrawell, Natalie E.; Dobson, Christopher M.; Wilson, Mark R.

2015-01-01

Alpha-2-macroglobulin is an abundant secreted protein that is of particular interest because of its diverse ligand binding profile and multifunctional nature, which includes roles as a protease inhibitor and as a molecular chaperone. The activities of alpha-2-macroglobulin are typically dependent on whether its conformation is native or transformed (i.e. adopts a more compact conformation after interactions with proteases or small nucleophiles), and are also influenced by dissociation of the native alpha-2-macroglobulin tetramer into stable dimers. Alpha-2-macroglobulin is predominately present as the native tetramer in vivo; once purified from human blood plasma, however, alpha-2-macroglobulin can undergo a number of conformational changes during storage, including transformation, aggregation or dissociation. We demonstrate that, particularly in the presence of sodium chloride or amine containing compounds, freezing and/or lyophilization of alpha-2-macroglobulin induces conformational changes with functional consequences. These conformational changes in alpha-2-macroglobulin are not always detected by standard native polyacrylamide gel electrophoresis, but can be measured using bisANS fluorescence assays. Increased surface hydrophobicity of alpha-2-macroglobulin, as assessed by bisANS fluorescence measurements, is accompanied by (i) reduced trypsin binding activity, (ii) increased chaperone activity, and (iii) increased binding to the surfaces of SH-SY5Y neurons, in part, via lipoprotein receptors. We show that sucrose (but not glycine) effectively protects native alpha-2-macroglobulin from denaturation during freezing and/or lyophilization, thereby providing a reproducible method for the handling and long-term storage of this protein. PMID:26103636

Cloning and characterization of profilin (Pru du 4), a cross-reactive almond (Prunus dulcis) allergen.

PubMed

Tawde, Pallavi; Venkatesh, Yeldur P; Wang, Fang; Teuber, Suzanne S; Sathe, Shridhar K; Roux, Kenneth H

2006-10-01

The identity of allergenic almond proteins is incomplete. Our objective was to characterize patient IgE reactivity to a recombinant and corresponding native almond allergen. An almond cDNA library was screened with sera from patients with allergy for IgE binding proteins. Two reactive clones were sequenced, and 1 was expressed. The expressed recombinant allergen and its native counterpart (purified from unprocessed almond flour) were assayed by 1-dimensional and 2-dimensional gel electrophoresis, dot blot, and ELISA, and screened for cross-reactivity with grass profilin. The 2 selected clones encoded profilin (designated Pru du 4) sequences that differed by 2 silent mutations. By dot-blot analyses, 6 of 18 patient sera (33%) reacted with the recombinant Pru du 4 protein, and 8 of 18 (44%) reacted with the native form. ELISA results were similar. Almond and ryegrass profilins were mutually inhibitable. Two-dimensional immunoblotting revealed the presence of more than 1 native almond profilin isoform. The strength of reactivity of some patients' serum IgE differed markedly between assays and between native and recombinant profilins. Almond nut profilin is an IgE-binding food protein that is cross-reactive with grass pollen profilin and is susceptible to denaturation, resulting in variable reactivity between assay types and between patients. Serum IgE of nearly half of the tested patients with almond allergy reacts with almond nut profilin. Because most patients also had pollinosis, the well-known cross-reactivity between pollen and food profilins could account for this pattern of reactivity.

Antitumor activity of Chlorella sorokiniana and Scenedesmus sp. microalgae native of Nuevo León State, México.

PubMed

Reyna-Martinez, Raul; Gomez-Flores, Ricardo; López-Chuken, Ulrico; Quintanilla-Licea, Ramiro; Caballero-Hernandez, Diana; Rodríguez-Padilla, Cristina; Beltrán-Rocha, Julio Cesar; Tamez-Guerra, Patricia

2018-01-01

Cancer cases result in 13% of all deaths worldwide. Unwanted side effects in patients under conventional treatments have led to the search for beneficial alternative therapies. Microalgae synthesize compounds with known in vitro and in vivo biological activity against different tumor cell lines. Therefore, native microalgae from the State of Nuevo Leon, Mexico may become a potential source of antitumor agents. The aim of the present study was to evaluate the in vitro cytotoxic effect of Nuevo Leon regional Chlorella sorokiniana (Chlorellales: Chlorellaceae) and Scenedesmus sp. (Chlorococcales: Scenedesmaceae). Native microalgae crude organic extracts cytotoxicity against murine L5178Y-R lymphoma cell line and normal lymphocyte proliferation were evaluated using the MTT reduction colorimetric assay. Cell death pathway was analyzed by acridine orange and ethidium bromide staining, DNA degradation in 2% agarose gel electrophoresis and caspases activity. Results indicated significant ( p  < 0.05) 61.89% ± 3.26% and 74.77% ± 1.84% tumor cytotoxicity by C. sorokiniana and Scenedesmus sp. methanol extracts, respectively, at 500 µg/mL, by the mechanism of apoptosis. This study contributes to Mexican microalgae biodiversity knowledge and their potential as antitumor agent sources.

Antitumor activity of Chlorella sorokiniana and Scenedesmus sp. microalgae native of Nuevo León State, México

PubMed Central

Beltrán-Rocha, Julio Cesar

2018-01-01

Cancer cases result in 13% of all deaths worldwide. Unwanted side effects in patients under conventional treatments have led to the search for beneficial alternative therapies. Microalgae synthesize compounds with known in vitro and in vivo biological activity against different tumor cell lines. Therefore, native microalgae from the State of Nuevo Leon, Mexico may become a potential source of antitumor agents. The aim of the present study was to evaluate the in vitro cytotoxic effect of Nuevo Leon regional Chlorella sorokiniana (Chlorellales: Chlorellaceae) and Scenedesmus sp. (Chlorococcales: Scenedesmaceae). Native microalgae crude organic extracts cytotoxicity against murine L5178Y-R lymphoma cell line and normal lymphocyte proliferation were evaluated using the MTT reduction colorimetric assay. Cell death pathway was analyzed by acridine orange and ethidium bromide staining, DNA degradation in 2% agarose gel electrophoresis and caspases activity. Results indicated significant (p < 0.05) 61.89% ± 3.26% and 74.77% ± 1.84% tumor cytotoxicity by C. sorokiniana and Scenedesmus sp. methanol extracts, respectively, at 500 µg/mL, by the mechanism of apoptosis. This study contributes to Mexican microalgae biodiversity knowledge and their potential as antitumor agent sources. PMID:29441241

Affinity in electrophoresis.

PubMed

Heegaard, Niels H H

2009-06-01

The journal Electrophoresis has greatly influenced my approaches to biomolecular affinity studies. The methods that I have chosen as my main tools to study interacting biomolecules--native gel and later capillary zone electrophoresis--have been the topic of numerous articles in Electrophoresis. Below, the role of the journal in the development and dissemination of these techniques and applications reviewed. Many exhaustive reviews on affinity electrophoresis and affinity CE have been published in the last few years and are not in any way replaced by the present deliberations that are focused on papers published by the journal.

Comparison of milk protein composition and rennet coagulation properties in native Swedish dairy cow breeds and high-yielding Swedish Red cows.

PubMed

Poulsen, Nina A; Glantz, Maria; Rosengaard, Anette K; Paulsson, Marie; Larsen, Lotte B

2017-11-01

Recent studies have reported a very high frequency of noncoagulating milk in Swedish Red cows. The underlying factors are not fully understood. In this study, we explored rennet-induced coagulation properties and relative protein profiles in milk from native Swedish Mountain and Swedish Red Polled cows and compared them with a subset of noncoagulating (NC) and well-coagulating (WC) milk samples from modern Swedish Red cows. The native breeds displayed a very low prevalence of NC milk and superior milk coagulation properties compared with Swedish Red cows. The predominant variants in both native breeds were α S1 -casein (α S1 -CN) B, β-CN A 2 and β-lactoglobulin (β-LG) B. For κ-CN, the B variant was predominant in the Swedish Mountain cows, whereas the A variant was the most frequent in the Swedish Red Polled. The native breeds displayed similar protein composition, but varied in content of α S1 -CN with 9 phosphorylated serines (9P) form. Within the Swedish Mountain cows, we observed a strong inverse correlation between the relative concentration of κ-CN and micelle size and a positive correlation between ionic calcium and gel firmness. For comparison, we investigated a subset of 29 NC and 28 WC milk samples, representing the extremes with regard to coagulation properties based on an initial screening of 395 Swedish Red cows. In Swedish Red, NC milk properties were found to be related to higher frequencies of β-CN A 2 , κ-CN E and A variants, as well as β-LG B, and the predominant composite genotype of β- and κ-CN in the NC group was A 2 A 2 /AA. Generally, the A 2 A 2 /AA composite genotype was related to lower relative concentrations of κ-CN isoforms and higher relative concentrations of α S1 -, α S2 -, and β-CN. Compared with the group of WC milk samples, NC milk contained a higher fraction of α S2 -CN and α-lactalbumin (α-LA) but a lower fraction of α S1 -CN 9P. In conclusion, milk from native Swedish breeds has good characteristics for cheese milk, which could be exploited in niche dairy products. In milk from Swedish Mountain cows, levels of ionic calcium seemed to be more important for rennet-induced gel firmness than variation in the relative protein profile. In Swedish Red, lower protein content as well as higher fraction of α S2 -CN and lower fraction of α S1 -CN 9P were related to NC milk. Further, a decrease in the frequency of the composite β-κ-CN genotype A 2 A 2 /AA through selective breeding could have a positive effect on milk coagulation properties. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Purification of two high molecular weight proteases from rabbit reticulocyte lysate

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

Hough, R.; Pratt, G.; Rechsteiner, M.

1987-05-01

The authors have purified two large proteases from rabbit reticulocyte lysate. The enzymes are so similar in their chromatographic behavior that each is the only significant contaminant of the other during the final stages of purification. At pH 7.8, both hydrolyze /sup 125/I-..cap alpha..-casein and 4-methylcoumaryl-7-amide (MCA) derivatives with tyrosine, phenylalanine or arginine at the P/sub 1/ position. The larger, ATP-dependent enzyme degrades ubiquitin-lysozyme conjugates, but it does not degrade unmodified lysozyme. Hydrolysis of Suc-Leu-Leu-Val-Tyr-MCA by this enzyme is also stimulated two-fold in the presence of ATP. The protease has a molecular weight of 950,000 based on sedimentation, gel filtrationmore » and non-denaturing PAGE. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the protease is composed of a number of subunits with molecular masses between 32 and 110 kDa. Densitometric analysis showed equivalent amounts of the two larger chains, and the presence of one copy of each in the native enzyme would be consistent with an M/sub r/ of 950,000. The smaller protease has a molecular weight of 700,000 and is composed of 8 to 10 subunits ranging from 21,000 to 32,000. It cleaves ubiquitin-lysozyme conjugates only slightly, and hydrolysis of conjugates or fluorogenic peptide substrates is not stimulated by ATP. This protease appears similar, if not identical, to the multicatalytic protease complex first purified by Wilk and Orlowski.« less

Purification, physicochemical characterization, and immunohistochemical localization of a major 11.7 S glycoprotein from the jelly coats of the anuran Lepidobatrachus laevis.

PubMed

Carroll, E J; Wei, S H; Nagel, G M

1991-02-01

Embryos of the frog Lepidobatrachus laevis are encased by a fertilization envelope and two jelly layers, termed J1 (innermost) and J2 (outermost). From preparations of total jelly solubilized from cleavage-stage embryos by a solution of alkaline beta-mercaptoethanol we have purified one jelly coat glycoprotein to homogeneity via FPLC gel permeation chromatography on Superose 6H. The purified glycoprotein was 94% protein and 6% carbohydrate, had an s0(20),w of 11.7 S, with a molecular weight of 245,000 measured by sedimentation equilibrium and 263,000 by gel permeation chromatography. SDS-PAGE revealed that the glycoprotein is composed of a single subunit near 29,700 molecular weight; thus we propose that eight of these subunits comprise the native molecule. Amino acid analysis of the glycoprotein indicated a high content of Glx + Asx (32.4 mole%), a low content of basic amino acids (Arg + Lys = 12.2 mole%), and a single cysteine residue per subunit. The N-terminal amino acid was threonine and the sequence of the first twenty amino acids was determined. Monospecific antisera to the glycoprotein were prepared in rabbits and were used to immunohistochemically localize the glycoprotein throughout the matrix of both jelly layers. Antiserum against the glycoprotein had virtually no effect on the fertilizability of jellied eggs in vitro; thus we hypothesize that the glycoprotein fulfills a structural role in both jelly layers.

Purification and Characterization of Caffeine Synthase from Tea Leaves1

PubMed Central

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

1999-01-01

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

Thermostable, salt tolerant, wide pH range novel chitobiase from Vibrio parahemolyticus: isolation, characterization, molecular cloning, and expression.

PubMed

Zhu, B C; Lo, J Y; Li, Y T; Li, S C; Jaynes, J M; Gildemeister, O S; Laine, R A; Ou, C Y

1992-07-01

A chitobiase gene from Vibrio parahemolyticus was cloned into plasmid pUC18 in Escherichia coli strain DH5 alpha. The plasmid construct, pC120, contained a 6.4 kb Vibrio DNA insert. The recombinant gene expressed chitobiase [EC 3.2.1.30] activity similar to that found in the native Vibrio. The enzyme was purified by ion exchange, hydroxylapatite and gel permeation chromatographies, and exhibited an apparent molecular weight of 80 kDa on SDS-polyacrylamide gel electrophoresis. Chitobiose and 6 more substrates, including beta-N-acetyl galactosamine glycosides, were hydrolyzed by the recombinant chitobiase, indicating its putative classification as an hexosaminidase [EC 3.2.1.52]. The enzyme was resistant to denaturation by 2 M NaCl, thermostable at 45 degrees C and active over a very unusual (for glycosyl hydrolases) pH range, from 4 to 10. The purified cloned chitobiase gave 4 closely focussed bands on an isoelectric focusing gel, at pH 4 to 6.5. The N-terminal 43 amino acid sequence shows no homology with other proteins in commercial databanks or in the literature, and from its N-terminal sequence, appears to be a novel protein, unrelated in sequence to chitobiases from other Vibrios reported and unrelated to hexosaminidases from other organisms.

Self healing hydrogels composed of amyloid nano fibrils for cell culture and stem cell differentiation.

PubMed

Jacob, Reeba S; Ghosh, Dhiman; Singh, Pradeep K; Basu, Santanu K; Jha, Narendra Nath; Das, Subhadeep; Sukul, Pradip K; Patil, Sachin; Sathaye, Sadhana; Kumar, Ashutosh; Chowdhury, Arindam; Malik, Sudip; Sen, Shamik; Maji, Samir K

2015-06-01

Amyloids are highly ordered protein/peptide aggregates associated with human diseases as well as various native biological functions. Given the diverse range of physiochemical properties of amyloids, we hypothesized that higher order amyloid self-assembly could be used for fabricating novel hydrogels for biomaterial applications. For proof of concept, we designed a series of peptides based on the high aggregation prone C-terminus of Aβ42, which is associated with Alzheimer's disease. These Fmoc protected peptides self assemble to β sheet rich nanofibrils, forming hydrogels that are thermoreversible, non-toxic and thixotropic. Mechanistic studies indicate that while hydrophobic, π-π interactions and hydrogen bonding drive amyloid network formation to form supramolecular gel structure, the exposed hydrophobic surface of amyloid fibrils may render thixotropicity to these gels. We have demonstrated the utility of these hydrogels in supporting cell attachment and spreading across a diverse range of cell types. Finally, by tuning the stiffness of these gels through modulation of peptide concentration and salt concentration these hydrogels could be used as scaffolds that can drive differentiation of mesenchymal stem cells. Taken together, our results indicate that small size, ease of custom synthesis, thixotropic nature makes these amyloid-based hydrogels ideally suited for biomaterial/nanotechnology applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Small acid soluble proteins for rapid spore identification.

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

Branda, Steven S.; Lane, Todd W.; VanderNoot, Victoria A.

2006-12-01

This one year LDRD addressed the problem of rapid characterization of bacterial spores such as those from the genus Bacillus, the group that contains pathogenic spores such as B. anthracis. In this effort we addressed the feasibility of using a proteomics based approach to spore characterization using a subset of conserved spore proteins known as the small acid soluble proteins or SASPs. We proposed developing techniques that built on our previous expertise in microseparations to rapidly characterize or identify spores. An alternative SASP extraction method was developed that was amenable to both the subsequent fluorescent labeling required for laser-induced fluorescencemore » detection and the low ionic strength requirements for isoelectric focusing. For the microseparations, both capillary isoelectric focusing and chip gel electrophoresis were employed. A variety of methods were evaluated to improve the molecular weight resolution for the SASPs, which are in a molecular weight range that is not well resolved by the current methods. Isoelectric focusing was optimized and employed to resolve the SASPs using UV absorbance detection. Proteomic signatures of native wild type Bacillus spores and clones genetically engineered to produce altered SASP patterns were assessed by slab gel electrophoresis, capillary isoelectric focusing with absorbance detection as well as microchip based gel electrophoresis employing sensitive laser-induced fluorescence detection.« less

Coating flow of an anti-HIV microbicide gel: boundary dilution and yield stress

NASA Astrophysics Data System (ADS)

Szeri, Andrew J.; Tasoglu, Savas; Park, Su Chan; Katz, David F.

2010-11-01

A recent study has confirmed, for the first time, that a vaginal gel formulation of the antiretroviral drug Tenofovir, when topically applied, significantly inhibits sexual HIV transmission to women [1]. However, the gel for this drug, and anti-HIV microbicide gels in general, have not been designed using an understanding of how gel spreading govern successful drug delivery. Elastohydrodynamic lubrication theory can be applied to model spreading of microbicide gels [2]. Here, we extend our initial analysis: we incorporate a yield stress, and we model the effects of gel dilution due to contact with vaginal fluid produced at the gel-tissue interface. Our model developed in [2] is supplemented with a convective-diffusive transport equation to characterize dilution, and solved using a multi-step scheme in a moving domain. The association between local dilution of gel and rheological properties is obtained experimentally. To model the common yield stress property of gels, we proceed by scaling analysis first. This establishes the conditions for validity of lubrication theory of a shear thinning yield stress fluid. This involves further development of the model in [2], incorporating a biviscosity model.[4pt] [1] Karim, et al., Science, 2010.[0pt] [2] Szeri, et al., Phy. of Fluids, 2008.

Low-molecular-weight gelators: elucidating the principles of gelation based on gelator solubility and a cooperative self-assembly model.

PubMed

Hirst, Andrew R; Coates, Ian A; Boucheteau, Thomas R; Miravet, Juan F; Escuder, Beatriu; Castelletto, Valeria; Hamley, Ian W; Smith, David K

2008-07-16

This paper highlights the key role played by solubility in influencing gelation and demonstrates that many facets of the gelation process depend on this vital parameter. In particular, we relate thermal stability ( T gel) and minimum gelation concentration (MGC) values of small-molecule gelation in terms of the solubility and cooperative self-assembly of gelator building blocks. By employing a van't Hoff analysis of solubility data, determined from simple NMR measurements, we are able to generate T calc values that reflect the calculated temperature for complete solubilization of the networked gelator. The concentration dependence of T calc allows the previously difficult to rationalize "plateau-region" thermal stability values to be elucidated in terms of gelator molecular design. This is demonstrated for a family of four gelators with lysine units attached to each end of an aliphatic diamine, with different peripheral groups (Z or Boc) in different locations on the periphery of the molecule. By tuning the peripheral protecting groups of the gelators, the solubility of the system is modified, which in turn controls the saturation point of the system and hence controls the concentration at which network formation takes place. We report that the critical concentration ( C crit) of gelator incorporated into the solid-phase sample-spanning network within the gel is invariant of gelator structural design. However, because some systems have higher solubilities, they are less effective gelators and require the application of higher total concentrations to achieve gelation, hence shedding light on the role of the MGC parameter in gelation. Furthermore, gelator structural design also modulates the level of cooperative self-assembly through solubility effects, as determined by applying a cooperative binding model to NMR data. Finally, the effect of gelator chemical design on the spatial organization of the networked gelator was probed by small-angle neutron and X-ray scattering (SANS/SAXS) on the native gel, and a tentative self-assembly model was proposed.

Antipeptide antibodies that can distinguish specific subunit polypeptides of glutamine synthetase from bean (Phaseolus vulgaris L.)

NASA Technical Reports Server (NTRS)

Cai, X.; Henry, R. L.; Takemoto, L. J.; Guikema, J. A.; Wong, P. P.; Spooner, B. S. (Principal Investigator)

1992-01-01

The amino acid sequences of the beta and gamma subunit polypeptides of glutamine synthetase from bean (Phaseolus vulgaris L.) root nodules are very similar. However, there are small regions within the sequences that are significantly different between the two polypeptides. The sequences between amino acids 2 and 9 and between 264 and 274 are examples. Three peptides (gamma 2-9, gamma 264-274, and beta 264-274) corresponding to these sequences were synthesized. Antibodies against these peptides were raised in rabbits and purified with corresponding peptide-Sepharose affinity chromatography. Western blot analysis of polyacrylamide gel electrophoresis of bean nodule proteins demonstrated that the anti-beta 264-274 antibodies reacted specifically with the beta polypeptide and the anti-gamma 264-274 and anti-gamma 2-9 antibodies reacted specifically with the gamma polypeptide of the native and denatured glutamine synthetase. These results showed the feasibility of using synthetic peptides in developing antibodies that are capable of distinguishing proteins with similar primary structures.

Identification of nonvolatile compounds in clove (Syzygium aromaticum) from Manado

NASA Astrophysics Data System (ADS)

Fathoni, A.; Saepudin, E.; Cahyana, A. H.; Rahayu, D. U. C.; Haib, J.

2017-07-01

Syzygium aromaticum (clove) are native to Indonesia and have been widely used in food industry due to their flavor. Nonvolatile compounds contribute to flavor, mainly in their taste. Currently, there is very little information available about nonvolatile compounds in clove. Identification of nonvolatile compounds is important to improve clove's value. Compound extraction was conducted by maceration in ethanol. Fractionations of the extract were performed by using gravity column chromatography on silica gel and Sephadex LH-20 as stationary phase. Nonvolatile compounds were identified by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). LC-MS/MS was operated in negative mode with 0.1 % formic acid in water and acetonitrile as mobile phase. Nonvolatile compounds were identified by fragment analysis and compared to references. Several compounds had been identified and characterized asquinic acid, monogalloylglucose, gallic acid, digalloylglucose, isobiflorin, biflorin, ellagic acid, hydroxygallic acid, luteolin, quercetin, naringenin, kaempferol, isorhamnetin, dimethoxyluteolin, and rhamnetin. These compounds had two main flavor perceptions, i.e. astringent, and bitter.

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms.

PubMed

Verhamme, Daniel T; Prosser, James I; Nicol, Graeme W

2011-06-01

The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH(4)(+)-N per gram of soil) and high (200 μg NH(4)(+)-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil.

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms

PubMed Central

Verhamme, Daniel T; Prosser, James I; Nicol, Graeme W

2011-01-01

The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH4+-N per gram of soil) and high (200 μg NH4+-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil. PMID:21228892

[Efficient extraction of transmembrane proteins using ProteoExtract Transmembrane Protein Extraction Kit].

PubMed

Błachnio, Karina

2010-01-01

Detergents commonly used for solubilization of membrane proteins may be ionic or non-ionic. Exposing membrane proteins to detergents, however, can adversely affect their native structure, which can be a major hindrance for functional studies. This is especially true for proteins with multiple transmembrane domains. The ProteoExtract Transmembrane Protein Extraction Kit (TM-PEK), offered by Merck, provides a detergent-free novel reagents to enable the mild and efficient extraction of proteins containing seven transmembrane domains, such as GPCRs (G-Protein Coupled Receptors) e.g.: Frizzled-4 and CELSR-3, from mammalian cells. The fraction enriched in transmembrane proteins using TM-PEK is directly compatible with enzyme assays, non-denaturing gel electrophoresis, 1- and 2-D SDS-PAGE, MS analysis, Western blotting, immunoprecipitation and ELISA. Unlike many alternatives, TM-PEK extraction procedure does not require sonication, extended rigorous vortexing, ultracentrifugation, or incubation of samples at elevated temperatures--thus minimizing the risk of post-extraction degradation or modifications.

Controlled release of vancomycin from thin sol-gel films on implant surfaces successfully controls osteomyelitis.

PubMed

Adams, Christopher S; Antoci, Valentin; Harrison, Gerald; Patal, Payal; Freeman, Terry A; Shapiro, Irving M; Parvizi, Javad; Hickok, Noreen J; Radin, Shula; Ducheyne, Paul

2009-06-01

Peri-prosthetic infection remains a serious complication of joint replacement surgery. Herein, we demonstrate that a vancomycin-containing sol-gel film on Ti alloy rods can successfully treat bacterial infections in an animal model. The vancomycin-containing sol-gel films exhibited predictable release kinetics, while significantly inhibiting S. aureus adhesion. When evaluated in a rat osteomyelitis model, microbiological analysis indicated that the vancomycin-containing sol-gel film caused a profound decrease in S. aureus number. Radiologically, while the control side showed extensive bone degradation, including abscesses and an extensive periosteal reaction, rods coated with the vancomycin-containing sol-gel film resulted in minimal signs of infection. MicroCT analysis confirmed the radiological results, while demonstrating that the vancomycin-containing sol-gel film significantly protected dense bone from resorption and minimized remodeling. These results clearly demonstrate that this novel thin sol-gel technology can be used for the targeted delivery of antibiotics for the treatment of periprosthetic as well as other bone infections. Copyright 2008 Orthopaedic Research Society

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.

Isolation of mitogenic substance from sclerotia of Sclerotinia sclerotiorum IFO 9395 extracted with phosphate buffer.

PubMed

Shinohara, H; Ohno, N; Yadomae, T

1991-05-01

The buffer extracts (3S) of sclerotia of Sclerotinia sclerotiorum IFO 9395 contained mitogenic substance(s) to murine splenocytes (Shinohara et al. Chem. Pharm. Bull., 38, 2219 (1990)). Although the native 3S was slightly mitogenic, heating of 3S induced significant mitogenic activity. To isolate the mitogen, we separated 3S by ion-exchange and gel filtration chromatographies. The isolated mitogen, named sclerogen, has a molecular mass of 32 kilodaltons (kDa) on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and the isoelectric point (pI) of 5.9 by chromatofocusing. Sclerogen was significantly mitogenic in vitro against murine splenocytes after heat denaturation, and also showed the augmentation of the primary mixed lymphocyte reaction (MLR) in vitro. However, sclerogen did not show the activation of an alternative pathway of complement and hemagglutination activity. These results suggest that sclerogen is a unique mitogen which differs from lectins and shows mitogenicity after heat denaturation.

Microheterogeneity in Purified Broad Bean Polyphenol Oxidase

PubMed Central

Ganesa, Chandrashekar; Fox, Mary T.; Flurkey, William H.

1992-01-01

Polyphenoloxidase was purified from chloroplasts of broad bean leaves (Vicia faba L.) to apparent homogeneity. The enzyme was composed of two proteins with an apparent mass of 65 and 68 kilodaltons after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The isolated enzyme contained covalently attached carbohydrates and bound concanavalin A, Phaseolus vulgaris erythroagglutinin, and Ricinus communis agglutinin lectins. Under native isoelectric focusing, several charged isoforms were present in the pH range of 4 to 6. Many, if not all, of the isoforms separated by isoelectric focusing were glycosylated and bound concanavalin A. All these isoforms shared a 65 kilodalton protein in common, and some of the isoforms were associated with both a 65 and 68 kilodalton protein. Isoforms separated by isoelectric focusing in the presence of 9 molar urea followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a similar pattern of proteins within a slightly higher pH range from 5 to 6.5. ImagesFigure 1Figure 2Figure 3Figure 4Figure 5Figure 6 PMID:16668664

Benzaldehyde lyase, a novel thiamine PPi-requiring enzyme, from Pseudomonas fluorescens biovar I.

PubMed Central

González, B; Vicuña, R

1989-01-01

Pseudomonas fluorescens biovar I can grow on benzoin as the sole carbon and energy source. This ability is due to benzaldehyde lyase, a new type of enzyme that irreversibly cleaves the acyloin linkage of benzoin, producing two molecules of benzaldehyde. Benzaldehyde lyase was purified 70-fold and found to require catalytic amounts of thiamine PPi (TPP) and a divalent cation as cofactors. Optimal activity was obtained with a 1.0 mM concentration of Mn2+, Mg2+, or Ca2+. Gel permeation chromatography indicated a native molecular weight of 80,000, whereas the enzyme migrated in sodium dodecyl sulfate-containing polyacrylamide gels as a single polypeptide with a molecular weight of 53,000. Benzaldehyde lyase is highly specific; of a variety of structurally related compounds tested, only benzoin and anisoin (4,4'-dimethoxybenzoin) acted as substrates, their apparent Kms being 9.0 x 10(-3) and 3.25 x 10(-2) mM, respectively. A catalytic mechanism for the enzyme is proposed. Images PMID:2496105

Integrated protocol for reliable and fast quantification and documentation of electrophoresis gels.

PubMed

Rehbein, Peter; Schwalbe, Harald

2015-06-01

Quantitative analysis of electrophoresis gels is an important part in molecular cloning, as well as in protein expression and purification. Parallel quantifications in yield and purity can be most conveniently obtained from densitometric analysis. This communication reports a comprehensive, reliable and simple protocol for gel quantification and documentation, applicable for single samples and with special features for protein expression screens. As major component of the protocol, the fully annotated code of a proprietary open source computer program for semi-automatic densitometric quantification of digitized electrophoresis gels is disclosed. The program ("GelQuant") is implemented for the C-based macro-language of the widespread integrated development environment of IGOR Pro. Copyright © 2014 Elsevier Inc. All rights reserved.

Structure Analysis of Jungle-Gym-Type Gels by Brownian Dynamics Simulation

NASA Astrophysics Data System (ADS)

Ohta, Noriyoshi; Ono, Kohki; Takasu, Masako; Furukawa, Hidemitsu

2008-02-01

We investigated the structure and the formation process of two kinds of gels by Brownian dynamics simulation. The effect of flexibility of main chain oligomer was studied. From our results, hard gel with rigid main chain forms more homogeneous network structure than soft gel with flexible main chain. In soft gel, many small loops are formed, and clusters tend to shrink. This heterogeneous network structure may be caused by microgels. In the low density case, soft gel shows more heterogeneity than the high density case.

Magnetic response of gelatin ferrogels across the sol-gel transition: the influence of high energy crosslinking on thermal stability.

PubMed

Wisotzki, Emilia I; Eberbeck, Dietmar; Kratz, Harald; Mayr, Stefan G

2016-05-07

As emerging responsive materials, ferrogels have demonstrated significant potential for applications in areas of engineering to regenerative medicine. Promising techniques to study the behavior of magnetic nanoparticles (MNPs) in such matrices include magnetic particle spectroscopy (MPS) and magnetorelaxometry (MRX). This work investigated the magnetic response of gelatin-based ferrogels with increasing temperatures, before and after high energy crosslinking. The particle response was characterized by the nonlinear magnetization using MPS and quasistatic magnetization measurements as well as MRX to discriminate between Néel and Brownian relaxation mechanisms. The effective magnetic response of MNPs in gelatin was suppressed, indicating that the magnetization of the ferrogels was strongly influenced by competing dipole-dipole interactions. Significant changes in the magnetic behavior were observed across the gelatin sol-gel transition, as influenced by the matrix viscosity. These relaxation processes were modeled by Fourier transformation of the Langevin function, combined with a Debye term for the nonlinear magnetic response, for single core MNPs embedded in matrices of changing viscosities. Using high energy electron irradiation as a crosslinking method, modified ferrogels exhibited thermal stability on a range of timescales. However, MRX relaxation times revealed a slight softening around the gelatin sol-gel transition felt by the smallest particles, demonstrating a high sensitivity to observe local changes in the viscoelasticity. Overall, MPS and MRX functioned as non-contact methods to observe changes in the nanorheology around the native sol-gel transition and in crosslinked ferrogels, as well as provided an understanding of how MNPs were integrated into and influenced by the surrounding matrix.

Strong Static Magnetic Fields Increase the Gel Signal in Partially Hydrated DPPC/DMPC Membranes.

PubMed

Tang, Jennifer; Alsop, Richard J; Schmalzl, Karin; Epand, Richard M; Rheinstädter, Maikel C

2015-09-29

NIt was recently reported that static magnetic fields increase lipid order in the hydrophobic membrane core of dehydrated native plant plasma membranes [Poinapen, Soft Matter 9:6804-6813, 2013]. As plasma membranes are multicomponent, highly complex structures, in order to elucidate the origin of this effect, we prepared model membranes consisting of a lipid species with low and high melting temperature. By controlling the temperature, bilayers coexisting of small gel and fluid domains were prepared as a basic model for the plasma membrane core. We studied molecular order in mixed lipid membranes made of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) using neutron diffraction in the presence of strong static magnetic fields up to 3.5 T. The contribution of the hydrophobic membrane core was highlighted through deuterium labeling the lipid acyl chains. There was no observable effect on lipid organization in fluid or gel domains at high hydration of the membranes. However, lipid order was found to be enhanced at a reduced relative humidity of 43%: a magnetic field of 3.5 T led to an increase of the gel signal in the diffraction patterns of 5%. While all biological materials have weak diamagnetic properties, the corresponding energy is too small to compete against thermal disorder or viscous effects in the case of lipid molecules. We tentatively propose that the interaction between the fatty acid chains' electric moment and the external magnetic field is driving the lipid tails in the hydrophobic membrane core into a better ordered state.

Crosslinkable hydrogels derived from cartilage, meniscus, and tendon tissue.

PubMed

Visser, Jetze; Levett, Peter A; te Moller, Nikae C R; Besems, Jeremy; Boere, Kristel W M; van Rijen, Mattie H P; de Grauw, Janny C; Dhert, Wouter J A; van Weeren, P René; Malda, Jos

2015-04-01

Decellularized tissues have proven to be versatile matrices for the engineering of tissues and organs. These matrices usually consist of collagens, matrix-specific proteins, and a set of largely undefined growth factors and signaling molecules. Although several decellularized tissues have found their way to clinical applications, their use in the engineering of cartilage tissue has only been explored to a limited extent. We set out to generate hydrogels from several tissue-derived matrices, as hydrogels are the current preferred cell carriers for cartilage repair. Equine cartilage, meniscus, and tendon tissue was harvested, decellularized, enzymatically digested, and functionalized with methacrylamide groups. After photo-cross-linking, these tissue digests were mechanically characterized. Next, gelatin methacrylamide (GelMA) hydrogel was functionalized with these methacrylated tissue digests. Equine chondrocytes and mesenchymal stromal cells (MSCs) (both from three donors) were encapsulated and cultured in vitro up to 6 weeks. Gene expression (COL1A1, COL2A1, ACAN, MMP-3, MMP-13, and MMP-14), cartilage-specific matrix formation, and hydrogel stiffness were analyzed after culture. The cartilage, meniscus, and tendon digests were successfully photo-cross-linked into hydrogels. The addition of the tissue-derived matrices to GelMA affected chondrogenic differentiation of MSCs, although no consequent improvement was demonstrated. For chondrocytes, the tissue-derived matrix gels performed worse compared to GelMA alone. This work demonstrates for the first time that native tissues can be processed into crosslinkable hydrogels for the engineering of tissues. Moreover, the differentiation of encapsulated cells can be influenced in these stable, decellularized matrix hydrogels.

Doxorubicin-loaded Zein in situ gel for interstitial chemotherapy.

PubMed

Cao, Xiaoying; Geng, Jianning; Su, Suwen; Zhang, Linan; Xu, Qian; Zhang, Li; Xie, Yinghua; Wu, Shaomei; Sun, Yongjun; Gao, Zibin

2012-01-01

A novel drug delivery system of doxorubicin (DOX)-loaded Zein in situ gel for interstitial chemotherapy was investigated in this study. The possible mechanisms of drug release were described according to morphological analysis by optical microscopy and scanning electronic microscope (SEM). In vitro and in vivo anti-tumor activity studies showed that DOX-loaded Zein in situ gel was superior to DOX solution. Local pharmacokinetics in tumor tissue was studied by quantitative analysis with confocal laser scanning microscopy (CLSM) combined with microdialysis technology. A pharmacokinetics mathematical model of DOX-loaded Zein in situ gel in tumors was then built.

Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics.

PubMed

Melani, Rafael D; Skinner, Owen S; Fornelli, Luca; Domont, Gilberto B; Compton, Philip D; Kelleher, Neil L

2016-07-01

Characterizing whole proteins by top-down proteomics avoids a step of inference encountered in the dominant bottom-up methodology when peptides are assembled computationally into proteins for identification. The direct interrogation of whole proteins and protein complexes from the venom of Ophiophagus hannah (king cobra) provides a sharply clarified view of toxin sequence variation, transit peptide cleavage sites and post-translational modifications (PTMs) likely critical for venom lethality. A tube-gel format for electrophoresis (called GELFrEE) and solution isoelectric focusing were used for protein fractionation prior to LC-MS/MS analysis resulting in 131 protein identifications (18 more than bottom-up) and a total of 184 proteoforms characterized from 14 protein toxin families. Operating both GELFrEE and mass spectrometry to preserve non-covalent interactions generated detailed information about two of the largest venom glycoprotein complexes: the homodimeric l-amino acid oxidase (∼130 kDa) and the multichain toxin cobra venom factor (∼147 kDa). The l-amino acid oxidase complex exhibited two clusters of multiproteoform complexes corresponding to the presence of 5 or 6 N-glycans moieties, each consistent with a distribution of N-acetyl hexosamines. Employing top-down proteomics in both native and denaturing modes provides unprecedented characterization of venom proteoforms and their complexes. A precise molecular inventory of venom proteins will propel the study of snake toxin variation and the targeted development of new antivenoms or other biotherapeutics. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Effect of thiolated polymers to textural and mucoadhesive properties of vaginal gel formulations prepared with polycarbophil and chitosan.

PubMed

Cevher, Erdal; Sensoy, Demet; Taha, Mohamed A M; Araman, Ahmet

2008-01-01

The aim of this study was to design and evaluate of mucoadhesive gel formulations for the vaginal application of clomiphene citrate (CLM) for local treatment of human papilloma virus (HPV) infections. Chitosan (CHI) and polycarbophil (PC) were covalently modified using the thioglycolic acid and L-cysteine, respectively. The formation of thiol conjugates of chitosan (CHI-TG) and polycarbophil (PC-CYS) were confirmed by FT-IR analysis and PC-CYS and CHI-TG were found to have 148.42 +/- 4.16 and 41.17 +/- 2.34 micromol of thiol groups per gram of polymer, respectively. One percent CLM gels were prepared by combination of various concentrations of PC and CHI with thiolated conjugates of these polymers. Hardness, compressibility, elasticity, adhesiveness and cohesiveness of the gels were measured by Texture profile analysis and the vaginal mucoadhesion was investigated by mucoadhesion test. The increasing in the amount of the thiol conjugates was found to enhance the elasticity, cohesiveness, adhesiveness and mucoadhesion of the gel formulations but not their hardness and compressibility when compared to gels prepared using their respective parent formulations. Slower release rate of CLM from gels was achieved when the polymer concentrations were increased in the gel formulations. PC and its thiol conjugate were found to prolong the release of CLM longer than 70 h unlike gel formulations prepared using CHI and its thiol conjugate which were able to release CLM up to 12 h. Stability of CLM was preserved during the 3 month stability analysis under controlled room temperature and accelerated conditions.

A combined analysis of 2 randomized clinical studies of tretinoin gel 0.05% for the treatment of acne.

PubMed

Webster, Guy; Cargill, D Innes; Quiring, John; Vogelson, Cullen T; Slade, Herbert B

2009-03-01

Acne vulgaris is a widely prevalent skin disorder primarily treated with retinoids, which have been shown to cause skin irritation. This report describes the combined analysis of 2 similar phase 3 studies designed to evaluate the efficacy and safety of an aqueous gel formulation of tretinoin relative to its vehicle (both studies) and a marketed microsphere formulation of tretinoin (one study) for once-daily topical treatment of acne. Randomized participants 10 years and older with mild to moderate acne (N=1537) received tretinoin gel 0.05% (n=674), tretinoin gel microsphere 0.1% (n=376), or vehicle (n=487) once daily for 12 weeks. Tretinoin gel was more effective than vehicle in reducing inflammatory (P<.001) and noninflammatory (P<.001) lesion counts over 12 weeks. Treatment success rate (global severity score, 0 or 1) was significantly greater in the tretinoin gel 0.05% group compared with the vehicle group (P<.001). The efficacy rate of tretinoin gel 0.05% was approximately 12% less than tretinoin gel microsphere 0.1%. Adverse events (AEs) were generally mild to moderate and rarely resulted in participant discontinuation. Incidence of skin-related AEs in the tretinoin gel 0.05% group (31%) was significantly lower compared with the tretinoin gel microsphere 0.1% group (52%)(P<.001). Thus, tretinoin gel 0.05% applied once daily is a well-tolerated and effective therapy for acne vulgaris and is associated with a low incidence of skin-related AEs.

Analysis of PEG oligomers in black gel inks: Discrimination and ink dating.

PubMed

Sun, Qiran; Luo, Yiwen; Xiang, Ping; Yang, Xu; Shen, Min

2017-08-01

Carbon-based black gel inks are common samples in forensic practice of questioned document examination in China, but there are few analytical methods for this type of ink. In this study, a liquid chromatography-.high resolution mass spectrometry (LC-HRMS) method was established for the analysis of PEG oligomers in carbon-based black gel ink entries. The coupled instruments achieve both the identification and quantification of PEG oligomers in ink entries with reproducible results. Twenty carbon-based black gel inks, whose Raman spectra appeared identical, were analyzed using the LC-HRMS method. As a result, the twenty gel inks were classified into four groups according to the distribution of PEG oligomers. Artificially aging of PEG 400 and a gel ink showed that as PEG degraded, the relative amounts of low molecular weight PEG oligomers increased, while those of high molecular weight decreased. The degradation of PEG oligomers in a naturally aged gel ink was consistent with those in the artificially aged samples, but occurred more slowly. This study not only provided a new method for discriminating carbon-based black gel ink entries, but also offered a new approach for studying the relative ink dating of carbon-based black gel ink entries. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

DIGE Analysis of Human Tissues.

PubMed

Gelfi, Cecilia; Capitanio, Daniele

2018-01-01

Two-dimensional difference gel electrophoresis (2-D DIGE) is an advanced and elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2-DE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The two-dye or three-dye systems can be adopted and their choice depends on specific applications. Furthermore, the use of an internal pooled standard makes 2-D DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. The image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.

Engineering of arteries in vitro

PubMed Central

Huang, Angela H.; Niklason, Laura E.

2014-01-01

This review will focus on two elements that are essential for functional arterial regeneration in vitro: the mechanical environment and the bioreactors used for tissue growth. The importance of the mechanical environment to embryological development, vascular functionality, and vascular graft regeneration will be discussed. Bioreactors generate mechanical stimuli to simulate the biomechanical environment of the arterial system. This system has been used to reconstruct arterial grafts with appropriate mechanical strength for implantation by controlling the chemical and mechanical environments in which the grafts are grown. Bioreactors are powerful tools to study the effect of mechanical stimuli on extracellular matrix (ECM) architecture and the mechanical properties of engineered vessels. Hence biomimetic systems enable us to optimize chemo-biomechanical culture conditions to regenerate engineered vessels with physiological properties similar to those of native arterial vessels. In addition, this review will introduce and examine various approaches and techniques that have been used to engineer biologically-based vascular grafts, including collagen-based grafts, fibrin-gel grafts, cell sheet engineering, biodegradable polymers, and decellularization of native vessels. PMID:24399290

Effects of citric acid esterification on digestibility, structural and physicochemical properties of cassava starch.

PubMed

Mei, Ji-Qiang; Zhou, Da-Nian; Jin, Zheng-Yu; Xu, Xue-Ming; Chen, Han-Qing

2015-11-15

In this study, citric acid was used to react with cassava starch in order to compare the digestibility, structural and physicochemical properties of citrate starch samples. The results indicated that citric acid esterification treatment significantly increased the content of resistant starch (RS) in starch samples. The swelling power and solubility of citrate starch samples were lower than those of native starch. Compared with native starch, a new peak at 1724 cm(-1) was appeared in all citrate starch samples, and crystalline peaks of all starch citrates became much smaller or even disappeared. Differential scanning calorimetry results indicated that the endothermic peak of citrate starches gradually shrank or even disappeared. Moreover, the citrate starch gels exhibited better freeze-thaw stability. These results suggested that citric acid esterification induced structural changes in cassava starch significantly affected its digestibility and it could be a potential method for the preparation of RS with thermal stability. Copyright © 2015 Elsevier Ltd. All rights reserved.

Influence of cross-linked arabinoxylans on the postprandial blood glucose response in rats.

PubMed

Vogel, Barbara; Gallaher, Daniel D; Bunzel, Mirko

2012-04-18

Viscous dietary fibers are well established to reduce the blood glucose response to a meal. In this study, arabinoxylans, the most abundant dietary fiber in most cereals, were extracted under alkaline conditions and cross-linked by using laccase. Cross-linking of the arabinoxylans led to gel formation and increased in vitro viscosity almost 100-fold after drying and rehydration. To determine the ability of these cross-linked arabinoxylans to blunt the postprandial blood glucose curve of a meal, arabinoxylans, either native or cross-linked, and either prehydrated or not, were fed to rats as part of a meal, and blood glucose was monitored at intervals after the meal. Cellulose, a nonviscous fiber, served as a control. Cross-linked, but not native, arabinoxylans significantly reduced the area under the blood glucose time curve 5-9% relative to cellulose, indicating that they remained viscous within the gastrointestinal tract, and thus likely provide the health benefits found with other viscous fibers.

Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines.

PubMed

Eastland, Adrienne; Hornick, Jessica; Kawamura, Ryo; Nanavati, Dhaval; Marko, John F

2016-09-01

We have found that reagents that reduce oxidized cysteines lead to destabilization of metaphase chromosome folding, suggesting that chemically linked cysteine residues may play a structural role in mitotic chromosome organization, in accord with classical studies by Dounce et al. (J Theor Biol 42:275-285, 1973) and Sumner (J Cell Sci 70:177-188, 1984a). Human chromosomes isolated into buffer unfold when exposed to dithiothreitol (DTT) or tris(2-carboxyethyl)phosphine (TCEP). In micromanipulation experiments which allow us to examine the mechanics of individual metaphase chromosomes, we have found that the gel-like elastic stiffness of native metaphase chromosomes is dramatically suppressed by DTT and TCEP, even before the chromosomes become appreciably unfolded. We also report protein labeling experiments on human metaphase chromosomes which allow us to tag oxidized and reduction-sensitive cysteine residues. PAGE analysis using fluorescent labels shows a small number of labeled bands. Mass spectrometry analysis of similarly labeled proteins provides a list of candidates for proteins with oxidized cysteines involved in chromosome organization, notably including components of condensin I, cohesin, the nucleosome-interacting proteins RCC1 and RCC2, as well as the RNA/DNA-binding protein NONO/p54NRB.

Subunit mass fingerprinting of mitochondrial complex I.

PubMed

Morgner, Nina; Zickermann, Volker; Kerscher, Stefan; Wittig, Ilka; Abdrakhmanova, Albina; Barth, Hans-Dieter; Brutschy, Bernhard; Brandt, Ulrich

2008-10-01

We have employed laser induced liquid bead ion desorption (LILBID) mass spectrometry to determine the total mass and to study the subunit composition of respiratory chain complex I from Yarrowia lipolytica. Using 5-10 pmol of purified complex I, we could assign all 40 known subunits of this membrane bound multiprotein complex to peaks in LILBID subunit fingerprint spectra by comparing predicted protein masses to observed ion masses. Notably, even the highly hydrophobic subunits encoded by the mitochondrial genome were easily detectable. Moreover, the LILBID approach allowed us to spot and correct several errors in the genome-derived protein sequences of complex I subunits. Typically, the masses of the individual subunits as determined by LILBID mass spectrometry were within 100 Da of the predicted values. For the first time, we demonstrate that LILBID spectrometry can be successfully applied to a complex I band eluted from a blue-native polyacrylamide gel, making small amounts of large multiprotein complexes accessible for subunit mass fingerprint analysis even if they are membrane bound. Thus, the LILBID subunit mass fingerprint method will be of great value for efficient proteomic analysis of complex I and its assembly intermediates, as well as of other water soluble and membrane bound multiprotein complexes.

Seed gum of Stryphnodendron barbatiman (Barbatimao)

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

Reicher, F.; Leitner, S.C.S.; Fontana, J.D.

1991-12-31

Stryphnodendron barbatiman (barbatimao) is a native tree that is found throughout the {open_quotes}Cerrados,{close_quotes} a region of Central Brazil. Plant seeds, on water extraction, furnished 28 g% galactomannan (dry-weight basis), the monosaccharide composition of which (galactose to mannose ratio, 1.0:1.5) fits in the legume heteromannan group. This seed gum, after Sevag deproteinization, still retained 6 g% of associated protein and had a molecular weight of about 1.8 MD on gel filtration. A high intrinsic viscosity (1300 cP) was observed for the polysaccharide sample obtained after reflux of the crushed seeds in 80% aqueous methanol.

Composites of silica with immobilized cholinesterase incorporated into polymeric shell

NASA Astrophysics Data System (ADS)

Payentko, Victoriya; Matkovsky, Alexander; Matrunchik, Yulia

2015-02-01

Synthetic approaches for new nanocomposite materials with relatively high cholinesterase activity have been developed. The peculiarity of the formation of such systems is the introduction of cholinesterase into polymer with subsequent incorporation on the ready-made silica particles and into the polysiloxane matrixes during sol-gel synthesis. Evaluation of the cholinesterase activity has been fulfilled through the imitation of the acetylcholine chloride decomposition reaction. Values of activity for cholinesterase nanocomposites demonstrated in this work are higher than those for the native cholinesterase. The higher activity of cholinesterase contained in nanocomposites was found for those prepared using highly dispersed silica.

Gelation and thermal characteristics of microwave extracted fish gelatin-natural gum composite gels.

PubMed

Binsi, P K; Nayak, Natasha; Sarkar, P C; Joshy, C G; Ninan, George; Ravishankar, C N

2017-02-01

In this study, the gelation and thermal characteristics of microwave extracted fish scale gelatin blended with natural gums such as gum arabic (AG), xanthan gum (XG), guar gum (GG), and tragacanth gum (TG) was evaluated. The nature of interaction and behavior of gelatin in presence of various gums was confirmed by particle size analysis, viscosity profile, FT-IR analysis and turbidity measurements. DSC data revealed that addition of AG, TG and GG remarkably improved the thermal stability of fish gelatin gel. The composite gels of TG, AG, and XG exhibited higher hardness and bloom strength values as compared to pure fish gelatin implying its textural synergy. Based on qualitative descriptive analysis, TG was found to be superior in improving the stability of fish gelatin gel, closely followed by AG. The results suggest that addition of these gums can reduce syneresis and retard melting of gelatin gels at ambient temperature, which are otherwise soft and thermally unstable.

Oligomeric State of Lipocalin-1 (LCN1) by Multiangle Laser Light Scattering and Fluorescence Anisotropy Decay

PubMed Central

Gasymov, Oktay K.; Abduragimov, Adil R.; Merschak, Petra; Redl, Bernhard; Glasgow, Ben J.

2007-01-01

Multiangle laser light scattering and fluorescence anisotropy decay measurements clarified the oligomeric states of native and recombinant tear lipocalin (lipocalin-1, TL). Native TL is monomeric. Recombinant TL (5-68 μM) with or without the histidine tag shows less than 7% dimer formation that is not in equilibrium with the monomeric form. Fluorescence anisotropy decay showed a correlation time of 9-10 ns for TL (10 μM- 1mM). Hydrodynamic calculations based on the crystallographic structure of a monomeric TL mutant closely concur with the observed correlation time. The solution properties calculated with HYDROPRO and SOLPRO programs from the available crystallographic structure of a monomeric TL mutant concur closely with the observed fluorescence anisotropy decay. The resulting model shows that protein topology is the major determinant of rotational correlation time and accounts for deviation from the Stokes-Einstein relation. The data challenge previous gel filtration studies to show that native TL exists predominantly as a monomer in solution rather than as a dimer. Delipidation of TL results in a formation of a complex oligomeric state (up to 25%). These findings are important as the dynamic processes in the tear film are limited by diffusional, translational as well as rotational, properties of the protein. PMID:17869594

Influence of grain activation conditions on functional characteristics of brown rice flour.

PubMed

Singh, Arashdeep; Sharma, Savita; Singh, Baljit

2017-09-01

Grain activation is a natural processing technique that can be used to produce modified flours without chemical modification. Functional characteristics of brown rice flour as influenced by grain activation time and temperatures were investigated. Germination temperatures at 25 ℃, 30 ℃ and 35 ℃ and time for 12, 24, 36 and 48 h significantly influenced the functional properties of flour with modification of starch, protein and high enzymatic activity. Significant decrease in the bulk density, water absorption and swelling power of brown rice flour was observed in comparison to non-germinated flour. Gel consistency and oil absorption capacity of brown rice flour increased as the grain activation time and temperature were increased. Native flour had lowest emulsion and foaming properties, while increase in grain activation time and temperature enhanced the emulsifying and foaming properties of flour. Paste clarity of native flour was 54% which was reduced to 25.17%; however, increase in germination time and temperature increased the % synersis values of germinated flour. Native flour had least gelation concentration of 12% which increased to 25% after 48 h of germination at 35 ℃. Overall, germination can be used as a natural way to modify the functional properties of brown rice flours for their utilization in variety food products.

Insightful understanding of the role of clay topology on the stability of biomimetic hybrid chitosan-clay thin films and CO2-dried porous aerogel microspheres.

PubMed

Frindy, Sana; Primo, Ana; Qaiss, Abou El Kacem; Bouhfid, Rachid; Lahcini, Mohamed; Garcia, Hermenegildo; Bousmina, Mosto; El Kadib, Abdelkrim

2016-08-01

Three natural clay-based microstructures, namely layered montmorillonite (MMT), nanotubular halloysite (HNT) and micro-fibrillar sepiolite (SP) were used for the synthesis of hybrid chitosan-clay thin films and porous aerogel microspheres. At a first glance, a decrease in the viscosity of the three gel-forming solutions was noticed as a result of breaking the mutual polymeric chains interaction by the clay microstructure. Upon casting, chitosan-clay films displayed enhanced hydrophilicity in the order CS

Data on DNA gel sample load, gel electrophoresis, PCR and cost analysis.

PubMed

Kuhn, Ramona; Böllmann, Jörg; Krahl, Kathrin; Bryant, Isaac Mbir; Martienssen, Marion

2018-02-01

The data presented in this article provide supporting information to the related research article "Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples" (Kuhn et al., 2017) [1]. In that article, we compared the suitability of ten selected DNA extraction methods based on DNA quality, purity, quantity and applicability to universal PCR. Here we provide the data on the specific DNA gel sample load, all unreported gel images of crude DNA and PCR results, and the complete cost analysis for all tested extraction procedures and in addition two commercial DNA extraction kits for soil and water.

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

PubMed

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

2011-01-01

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

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

PubMed Central

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

1984-01-01

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

PFGE MAPPER and PFGE READER: two tools to aid in the analysis and data input of pulse field gel electrophoresis maps.

PubMed Central

Shifman, M. A.; Nadkarni, P.; Miller, P. L.

1992-01-01

Pulse field gel electrophoresis mapping is an important technique for characterizing large segments of DNA. We have developed two tools to aid in the construction of pulse field electrophoresis gel maps: PFGE READER which stores experimental conditions and calculates fragment sizes and PFGE MAPPER which constructs pulse field gel electrophoresis maps. PMID:1482898

Acylhydrazone bond dynamic covalent polymer gel monolithic column online coupling to high-performance liquid chromatography for analysis of sulfonamides and fluorescent whitening agents in food.

PubMed

Zhang, Chengjiang; Luo, Xialin; Wei, Tianfu; Hu, Yufei; Li, Gongke; Zhang, Zhuomin

2017-10-13

A new dynamic covalent polymer (DCP) gel was well designed and constructed based on imine chemistry. Polycondensation of 4,4'-biphenyldicarboxaldehyde and 1,3,5-benzenetricarbohydrazide via Schiff-base reaction resulted in an acylhydrazone bond gel (AB-gel) DCP. AB-gel DCP had three-dimensional network of interconnected nanoparticles with hierarchically porous structure. AB-gel DCP was successfully fabricated as a monolithic column by an in-situ chemical bonding method for online enrichment and separation purpose with excellent permeability. AB-gel DCP based monolithic column showed remarkable adsorption affinity towards target analytes including sulfonamides (SAs) and fluorescent whitening agents (FWAs) due to its strong π-π affinity, hydrophobic effect and hydrogen bonding interaction. Then, AB-gel DCP based monolithic column was applied for online separation and analysis of trace SAs and FWAs in food samples coupled with high-performance liquid chromatography (HPLC). Sulfathiazole (ST) and sulfadimidine (SM2) in one positive weever sample were actually found and determined with concentrations of 273.8 and 286.3μg/kg, respectively. 2,5-Bis(5-tert-butyl-2-benzoxazolyl) thiophene (FWA184) was actually quantified in one tea infusion sample with the concentration of 268.5ng/L. The spiked experiments suggested the good recoveries in range of 74.5-110% for SAs in weever and shrimp samples with relative standard deviations (RSDs) less than 9.7% and in range of 74.0-113% for FWAs in milk and tea infusion samples with RSDs less than 9.0%. AB-gel DCP monolithic column was proved to be a promising sample preparation medium for online separation and analysis of trace analytes in food samples with complex matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

Sol-gel titania-coated needles for solid phase dynamic extraction-GC/MS analysis of desomorphine and desocodeine.

PubMed

Su, Chi-Ju; Srimurugan, Sankarewaran; Chen, Chinpiao; Shu, Hun-Chi

2011-01-01

Novel sol-gel titania film coated needles for solid-phase dynamic extraction (SPDE)-GC/MS analysis of desomorphine and desocodeine are described. The high thermal stability of titania film permits efficient extraction and analysis of poorly volatile opiate drugs. The influences of sol-gel reaction time, coating layer, extraction and desorption time and temperature on the SPDE needle performance were investigated. The deuterium labeled internal standard was introduced either during the extraction of analyte or directly injected to GC after the extraction process. The latter method was shown to be more sensitive for the analysis of water and urine samples containing opiate drugs. The proposed conditions provided a wide linear range (from 5-5000 ppb), and satisfactory linearity, with R(2) values from 0.9958 to 0.9999, and prominent sensitivity, LOQs (1.0-5.0 ng/g). The sol-gel titania film coated needle with SPDE-GC/MS will be a promising technique for desomorphine and desocodeine analysis in urine.

Genetic and biochemical characterization of the GH72 family of cell wall transglycosylases in Neurospora crassa.

PubMed

Ao, Jie; Free, Stephen J

2017-04-01

The Neurospora crassa genome encodes five GH72 family transglycosylases, and four of these enzymes (GEL-1, GEL-2, GEL-3 and GEL-5) have been found to be present in the cell wall proteome. We carried out an extensive genetic analysis on the role of these four transglycosylases in cell wall biogenesis and demonstrated that the transglycosylases are required for the formation of a normal cell wall. As suggested by the proteomic analysis, we found that multiple transglycosylases were being expressed in N. crassa cells and that different combinations of the enzymes are required in different cell types. The combination of GEL-1, GEL-2 and GEL-5 is required for the growth of vegetative hyphae, while the GEL-1, GEL-2, GEL-3 combination is needed for the production of aerial hyphae and conidia. Our data demonstrates that the enzymes are redundant with partially overlapping enzymatic activities, which provides the fungus with a robust cell wall biosynthetic system. Characterization of the transglycosylase-deficient mutants demonstrated that the incorporation of cell wall proteins was severely compromised. Interestingly, we found that the transglycosylase-deficient mutant cell walls contained more β-1,3-glucan than the wild type cell wall. Our results demonstrate that the GH72 transglycosylases are not needed for the incorporation of β-1,3-glucan into the cell wall, but they are required for the incorporation of cell wall glycoprotein into the cell wall. Copyright © 2017 Elsevier Inc. All rights reserved.

Low-cost conversion of the Polaroid MD-4 land camera to a digital gel documentation system.

PubMed

Porch, Timothy G; Erpelding, John E

2006-04-30

A simple, inexpensive design is presented for the rapid conversion of the popular MD-4 Polaroid land camera to a high quality digital gel documentation system. Images of ethidium bromide stained DNA gels captured using the digital system were compared to images captured on Polaroid instant film. Resolution and sensitivity were enhanced using the digital system. In addition to the low cost and superior image quality of the digital system, there is also the added convenience of real-time image viewing through the swivel LCD of the digital camera, wide flexibility of gel sizes, accurate automatic focusing, variable image resolution, and consistent ease of use and quality. Images can be directly imported to a computer by using the USB port on the digital camera, further enhancing the potential of the digital system for documentation, analysis, and archiving. The system is appropriate for use as a start-up gel documentation system and for routine gel analysis.

Optimization of Large Gel 2D Electrophoresis for Proteomic Studies of Skeletal Muscle

PubMed Central

Reed, Patrick W.; Densmore, Allison; Bloch, Robert J.

2013-01-01

We describe improved methods for large format, 2-dimensional gel electrophoresis (2-DE) that improve protein solubility and recovery, minimize proteolysis, and reduce the loss of resolution due to contaminants and manipulations of the gels, and thus enhance quantitative analysis of protein spots. Key modifications are: (i) the use of 7M urea + 2 M thiourea, instead of 9M urea, in sample preparation and in the tops of the gel tubes; (ii) standardized deionization of all solutions containing urea with a mixed bed ion exchange resin and removal of urea from the electrode solutions; and (iii) use of a new gel tank and cooling device that eliminate the need to run two separating gels in the SDS dimension. These changes make 2D-GE analysis more reproducible and sensitive, with minimal artifacts. Application of this method to the soluble fraction of muscle tissues reliably resolves ~1800 protein spots in adult human skeletal muscle and over 2800 spots in myotubes. PMID:22589104

Selective Extraction and Purification of Azaspiracids from Blue Mussels ( Mytilus edulis) Using Boric Acid Gel.

PubMed

Miles, Christopher O; Kilcoyne, Jane; McCarron, Pearse; Giddings, Sabrina D; Waaler, Thor; Rundberget, Thomas; Samdal, Ingunn A; Løvberg, Kjersti E

2018-03-21

Azaspiracids belong to a family of more than 50 polyether toxins originating from marine dinoflagellates such as Azadinium spinosum. All of the azaspiracids reported thus far contain a 21,22-dihydroxy group. Boric acid gel can bind selectively to compounds containing vic-diols or α-hydroxycarboxylic acids via formation of reversible boronate complexes. Here we report use of the gel to selectively capture and release azaspiracids from extracts of blue mussels. Analysis of the extracts and fractions by liquid chromatography-tandem mass spectrometry (LC-MS) showed that this procedure resulted in an excellent cleanup of the azaspiracids in the extract. Analysis by enzyme-linked immunoasorbent assay (ELISA) and LC-MS indicated that most azaspiracid analogues were recovered in good yield by this procedure. The capacity of boric acid gel for azaspiracids was at least 50 μg/g, making this procedure suitable for use in the early stages of preparative purification of azaspiracids. In addition to its potential for concentration of dilute samples, the extensive cleanup provided by boric acid gel fractionation of azaspiracids in mussel samples almost eliminated matrix effects during subsequent LC-MS and could be expected to reduce matrix effects during ELISA analysis. The method may therefore prove useful for quantitative analysis of azaspiracids as part of monitoring programs. Although LC-MS data showed that okadaic acid analogues also bound to the gel, this was much less efficient than for azaspiracids under the conditions used. The boric acid gel methodology is potentially applicable to other important groups of natural toxins containing diols including ciguatoxins, palytoxins, pectenotoxins, tetrodotoxin, trichothecenes, and toxin glycosides.

Physiology and enzymology involved in denitrification by Shewanella putrefaciens

NASA Technical Reports Server (NTRS)

Krause, B.; Nealson, K. H.

1997-01-01

Nitrate reduction to N2O was investigated in batch cultures of Shewanella putrefaciens MR-1, MR-4, and MR-7. All three strains reduced nitrate to nitrite to N2O, and this reduction was coupled to growth, whereas ammonium accumulation was very low (0 to 1 micromol liter-1). All S. putrefaciens isolates were also capable of reducing nitrate aerobically; under anaerobic conditions, nitrite levels were three- to sixfold higher than those found under oxic conditions. Nitrate reductase activities (31 to 60 micromol of nitrite min-1 mg of protein-1) detected in intact cells of S. putrefaciens were equal to or higher than those seen in Escherichia coli LE 392. Km values for nitrate reduction ranged from 12 mM for MR-1 to 1.3 mM for MR-4 with benzyl viologen as an artifical electron donor. Nitrate and nitrite reductase activities in cell-free preparations were demonstrated in native gels by using reduced benzyl viologen. Detergent treatment of crude and membrane extracts suggested that the nitrate reductases of MR-1 and MR-4 are membrane bound. When the nitrate reductase in MR-1 was partially purified, three subunits (90, 70, and 55 kDa) were detected in denaturing gels. The nitrite reductase of MR-1 is also membrane bound and appeared as a 60-kDa band in sodium dodecyl sulfate-polyacrylamide gels after partial purification.

Screening trematodes for novel intervention targets: a proteomic and immunological comparison of Schistosoma haematobium, Schistosoma bovis and Echinostoma caproni

PubMed Central

HIGÓN, MELISSA; COWAN, GRAEME; NAUSCH, NORMAN; CAVANAGH, DAVID; OLEAGA, ANA; TOLEDO, RAFAEL; STOTHARD, J. RUSSELL; ANTÚNEZ, ORETO; MARCILLA, ANTONIO; BURCHMORE, RICHARD; MUTAPI, FRANCISCA

2011-01-01

SUMMARY With the current paucity of vaccine targets for parasitic diseases, particularly those in childhood, the aim of this study was to compare protein expression and immune cross-reactivity between the trematodes Schistosoma haematobium, S. bovis and Echinostoma caproni in the hope of identifying novel intervention targets. Native adult parasite proteins were separated by 2-dimensional gel electrophoresis and identified through electrospray ionisation tandem mass spectrometry to produce a reference gel. Proteins from differential gel electrophoresis analyses of the three parasite proteomes were compared and screened against sera from hamsters infected with S. haematobium and E. caproni following 2-dimensional Western blotting. Differential protein expression between the three species was observed with circa 5% of proteins from S. haematobium showing expression up-regulation compared to the other two species. There was 91% similarity between the proteomes of the two Schistosoma species and 81% and 78·6% similarity between S. haematobium and S. bovis versus E. caproni, respectively. Although there were some common cross-species antigens, species-species targets were revealed which, despite evolutionary homology, could be due to phenotypic plasticity arising from different host-parasite relationships. Nevertheless, this approach helps to identify novel intervention targets which could be used as broad-spectrum candidates for future use in human and veterinary vaccines. PMID:21729355

Further characterization of the cold agglutinin from the snail Achatina fulica.

PubMed Central

Mitra, D; Sarkar, M; Allen, A K

1987-01-01

The cold agglutinin from the albumin gland of the snail Achatina fulica was purified to homogeneity by using sheep gastric mucin-Sepharose 4B as affinity column followed by gel filtration on Bio-Gel P-300. The homogeneity was checked by alkaline gel electrophoresis, immunodiffusion and immunoelectrophoresis. The purified cold agglutinin is a glycoprotein of native M2 220,000 consisting of three non-covalently bound subunits of Mr 84,000, 74,000 and 62,000 and having a pI value of 4.5. The predominant amino acids are aspartic acid and glutamic acid (or amides) and serine, which account for 39% of the residues. About 3% of the residues are half-cystine. The lectin is a glycoprotein with about 30.7% carbohydrate, the most abundant sugars being galactose, N-acetylgalactosamine and N-acetylglucosamine. Mannose, xylose and fucose are also present. The inhibition of agglutination of human umbilical-cord erythrocytes by the cold agglutinin is specific for methyl beta-D-galactoside and also for glycolipids present on cord erythrocytes. The c.d. data show only negative ellipticity values in the far-u.v. region for the protein at various concentrations and temperatures and also in the presence of the hapten lactose (at different concentrations), indicating the presence of a random-coil conformation in the agglutinin that varies according to temperature. Images Fig. 2. Fig. 3. Fig. 5. Fig. 6. PMID:3593252

A tetrodotoxin-binding protein in the hemolymph of shore crab Hemigrapsus sanguineus: purification and properties.

PubMed

Nagashima, Yuji; Yamamoto, Kazuhiko; Shimakura, Kuniyoshi; Shiomi, Kazuo

2002-06-01

The shore crab Hemigrapsus sanguineus hemolymph contains soluble proteins that bind tetrodotoxin (TTX) and are responsible for high resistance of the crab to TTX. The TTX-binding protein was purified from the hemolymph by ultrafiltration, lectin affinity chromatography and gel filtration HPLC. The purified protein gave only one band in native-polyacrylamide gel electrophoresis (PAGE), confirming its homogeneity. Its molecular weight was estimated to be about 400k by gel filtration HPLC, while it was estimated to be about 82k under non-reducing conditions and about 72 and 82k under reducing conditions by SDS-PAGE, indicating that the TTX-binding protein was composed of at least two distinct subunits. The TTX-binding protein was an acidic glycoprotein with pI 3.5, abundant in Asp and Glu but absent in Trp, and contained 6% reducing sugar and 12% amino sugar. The protein selectively bound to TTX, with a neutralizing ability of 6.7 mouse unit TTX/mg protein, but not to paralytic shellfish poisoning toxins. However, its neutralizing activity was almost lost by treatments with enzymes (protease XIV, thermolysin, trypsin, amyloglucosidase and alpha-amylase) and denaturing agents (1% SDS, 1% dithiothreitol, 8 M urea and 6 M guanidine hydrochloride), suggesting the involvement of both proteinaceous and sugar moieties in the binding to TTX and the importance of the steric conformation of the TTX-binding protein. Copright 2002 Elsevier Science Ltd.

Surface analysis and biocorrosion properties of nanostructured surface sol-gel coatings on Ti6Al4V titanium alloy implants.

PubMed

Advincula, Maria C; Petersen, Don; Rahemtulla, Firoz; Advincula, Rigoberto; Lemons, Jack E

2007-01-01

Surfaces of biocompatible alloys used as implants play a significant role in their osseointegration. Surface sol-gel processing (SSP), a variant of the bulk sol-gel technique, is a relatively new process to prepare bioreactive nanostructured titanium oxide for thin film coatings. The surface topography, roughness, and composition of sol-gel processed Ti6Al4V titanium alloy coatings was investigated by atomic force microscopy (AFM) and X-ray electron spectroscopy (XPS). This was correlated with corrosion properties, adhesive strength, and bioreactivity in simulated body fluids (SBF). Electroimpedance spectroscopy (EIS) and polarization studies indicated similar advantageous corrosion properties between sol-gel coated and uncoated Ti6Al4V, which was attributed to the stable TiO2 composition, topography, and adhesive strength of the sol-gel coating. In addition, inductive coupled plasma (ICP) and scanning electron microscopy with energy dispersive spectrometry (SEM-EDS) analysis of substrates immersed in SBF revealed higher deposition of calcium and phosphate and low release rates of alloying elements from the sol-gel modified alloys. The equivalent corrosion behavior and the definite increase in nucleation of calcium apatite indicate the potential of the sol-gel coating for enhanced bioimplant applications. 2006 Wiley Periodicals, Inc.

Comparative Evaluation of Pain Scores during Periodontal Probing with or without Anesthetic Gels.

PubMed

Mishra, Ashank; Priyanka, Mandapathi; Pradeep, Koppolu; Reddy Pathakota, Krishnajaneya

2016-01-01

Context. The initial periodontal examination which includes full-mouth periodontal probing is one of the discomforting procedures for a patient. Aim. To evaluate the efficacy of two local anesthetic gels in the reduction of pain during periodontal probing using Florida probe in CGP patients in comparison with manual probing. Materials and Methods. Ninety systemically healthy patients with moderate to severe CGP patients were recruited. In each patient, the quadrants were randomly assigned to manual probing with UNC-15 probe, probing with Florida probe, and Florida probing with lidocaine 10% gel and with benzocaine 20% gel. In the quadrants undergoing probing with anesthetic gels, the sites were isolated and the gel was injected using syringe and a blunt-end cannula. Pain was measured using 10 mm horizontal VAS. Statistical Analysis. The analysis was carried out using SPSS version 18. The comparison of mean VAS scores was done using repeated measures ANOVA with post hoc Bonferroni test. Results. Mean VAS for manual probing was significantly more than Florida probing. Further, the mean VAS score for Florida probing was higher than the two gels. Conclusion. It is suggested that the gels might be useful in reducing pain experienced during full-mouth periodontal probing in patients with CGP.

Peripheral stator of the yeast V-ATPase: stoichiometry and specificity of interaction between the EG complex and subunits C and H.

PubMed

Féthière, James; Venzke, David; Madden, Dean R; Böttcher, Bettina

2005-12-06

V-ATPases are multisubunit membrane protein complexes that use the energy provided by ATP hydrolysis to generate a proton gradient across various intracellular and plasma membranes. In doing so, they maintain an acidic pH in the lumen of intracellular organelles and acidify extracellular milieu to support specific cellular functions. V-ATPases are structurally similar to the F1F0-ATP synthase, with an intrinsic membrane domain (V0) and an extrinsic peripheral domain (V1) joined by several connecting elements. To gain a clear functional understanding of the catalytic mechanism, and of the stability requirements for regulatory processes in the enzyme, a clear topology of the enzyme has to be established. In particular, the composition and arrangement of the peripheral stator subunits must be firmly settled, as these play specific roles in catalysis and regulation. We have designed a strategy allowing us to coexpress different combinations of these subunits to delineate specific interactions. In this study, we report the interaction between the peripheral stator EG complex and subunits C and H of the V-ATPase from the yeast Saccharomyces cerevisae. A combination of analytical gel filtration, native gel electrophoresis, and ultracentrifugation analysis allowed us to ascertain the homogeneity and molar mass of the purified EGC complex as well as of the EG complex, supporting the formation of 1:1(:1) stoichiometric complexes. The EGC complex can be formed in vitro by combining equimolar amounts of subunit C and the EG subcomplex and results most likely from the initial interaction between subunits E and C.

Heterologous expression and characterization of a glucose-stimulated β-glucosidase from the termite Neotermes koshunensis in Aspergillus oryzae.

PubMed

Uchima, Cristiane Akemi; Tokuda, Gaku; Watanabe, Hirofumi; Kitamoto, Katsuhiko; Arioka, Manabu

2011-03-01

Neotermes koshunensis is a lower termite that secretes endogenous β-glucosidase in the salivary glands. This β-glucosidase (G1NkBG) was successfully expressed in Aspergillus oryzae. G1NkBG was purified to homogeneity from the culture supernatant through ammonium sulfate precipitation and anion exchange, hydrophobic, and gel filtration chromatographies with a 48-fold increase in purity. The molecular mass of the native enzyme appeared as a single band at 60 kDa after gel filtration analysis, indicating that G1NkBG is a monomeric protein. Maximum activity was observed at 50 °C with an optimum pH at 5.0. G1NkBG retained 80% of its maximum activity at temperatures up to 45 °C and lost its activity at temperatures above 55 °C. The enzyme was stable from pH 5.0 to 9.0. G1NkBG was most active towards laminaribiose and p-nitrophenyl-β-D-fucopyranoside. Cellobiose, as well as cello-oligosaccharides, was also well hydrolyzed. The enzyme activity was slightly stimulated by Mn(2+) and glycerol. The K(m) and V(max) values were 0.77 mM and 16 U/mg, respectively, against p-nitrophenyl-β-D-glucopyranoside. An unusual finding was that G1NkBG was stimulated by 1.3-fold when glucose was present in the reaction mixture at a concentration of 200 mM. These characteristics, particularly the stimulation of enzyme activity by glucose, make G1NkBG of great interest for biotechnological applications, especially for bioethanol production.

Enzymatic, antimicrobial and toxicity studies of the aqueous extract of Ananas comosus (pineapple) crown leaf.

PubMed

Dutta, Sangita; Bhattacharyya, Debasish

2013-11-25

Various parts of the plant pineapple (Ananas comosus) are used in traditional medicine worldwide for treatment of a number of diseases and disorders. In folk medicine, pineapple leaf extract was used as an antimicrobial, vermicide, purgative, emmenagoogue, abortifacient, anti-oedema and anti-inflammatory agent. Compared to the fruit and stem extracts of pineapple, information about its leaf extract is limited. The potential of pineapple crown leaf extract as an ethno-medicine has been evaluated in terms of its enzymatic activities related to wound healing, antimicrobial property and toxicity. Major protein components of the extract were revealed by 2-D gel electrophoresis followed by MS/MS analysis. Zymography, DQ-gelatin assay were performed to demonstrate proteolytic, fibrinolytic, gelatinase and collagenase activities. DNase and RNase activities were revealed from agarose gel electrophoresis. Antimicrobial activity was evaluated spectrophotometrically from growth inhibition. Sprague-Dawley rat model was used to measure acute and sub-acute toxicity of the extract by analyzing blood markers. The extract contains several proteins that were clustered under native condition. Proteomic studies indicated presence of fruit bromelain as major protein constituent of the extract. It showed nonspecific protease activity, gelatinolytic, collagenase, fibrinolytic, acid and alkaline phosphatase, peroxidase, DNase and RNase activities along with considerable anti-microbial property. The leaf extract did not induce any toxicity in rats after oral administration of acute and sub-acute doses. Pineapple leaf extract is nontoxic, contains enzymes related to damage tissue repairing, wound healing and possibly prevents secondary infections from microbial organisms. © 2013 Elsevier Ireland Ltd. All rights reserved.

PCR amplification on microarrays of gel immobilized oligonucleotides

DOEpatents

Strizhkov, Boris; Tillib, Sergei; Mikhailovich, Vladimir; Mirzabekov, Andrei

2003-11-04

The invention relates two general methods for performing PCR amplification, combined with the detection and analysis of the PCR products on a microchip. In the first method, the amplification occurs both outside and within a plurality of gel pads on a microchip, with at least one oligonucleotide primer immobilized in a gel pad. In the second method, PCR amplification also takes place within gel pads on a microchip, but the pads are surrounded by a hydrophobic liquid such as that which separates the individual gel pads into environments which resemble micro-miniaturized test tubes.

From kinetic-structure analysis to engineering crystalline fiber networks in soft materials.

PubMed

Wang, Rong-Yao; Wang, Peng; Li, Jing-Liang; Yuan, Bing; Liu, Yu; Li, Li; Liu, Xiang-Yang

2013-03-07

Understanding the role of kinetics in fiber network microstructure formation is of considerable importance in engineering gel materials to achieve their optimized performances/functionalities. In this work, we present a new approach for kinetic-structure analysis for fibrous gel materials. In this method, kinetic data is acquired using a rheology technique and is analyzed in terms of an extended Dickinson model in which the scaling behaviors of dynamic rheological properties in the gelation process are taken into account. It enables us to extract the structural parameter, i.e. the fractal dimension, of a fibrous gel from the dynamic rheological measurement of the gelation process, and to establish the kinetic-structure relationship suitable for both dilute and concentrated gelling systems. In comparison to the fractal analysis method reported in a previous study, our method is advantageous due to its general validity for a wide range of fractal structures of fibrous gels, from a highly compact network of the spherulitic domains to an open fibrous network structure. With such a kinetic-structure analysis, we can gain a quantitative understanding of the role of kinetic control in engineering the microstructure of the fiber network in gel materials.

Gel properties and interactions of Mesona blumes polysaccharide-soy protein isolates mixed gel: The effect of salt addition.

PubMed

Wang, Wenjie; Shen, Mingyue; Liu, Suchen; Jiang, Lian; Song, Qianqian; Xie, Jianhua

2018-07-15

Effect of different salt ions on the gel properties and microstructure of Mesona blumes polysaccharide (MBP)-soy protein isolates (SPI) mixed gels were investigated. Sodium and calcium ions were chosen to explore their effects on the rheological behavior and gel properties of MBP-SPI mixed gels were evaluated by using rheological, X-ray diffraction, protein solubility determination, and microstructure analysis. Results showed that the addition of salt ions change the crystalline state of gels system, the crystal of gel was enhanced at low ion concentrations (0.005-0.01 M). The two peaks of gel characteristic at 8.9° and 19.9° almost disappeared at high salt ions concentrations (0.015-0.02 M), and new crystallization peaks appeared at around 30° and 45°. The elasticity, viscosity, gel strength, water holding capacity, and thermal stability of gel were increased at low ion concentration. Results showed that the main interactions which promoted gel formation and maintain the three-dimensional structure of the gel were electrostatic interactions, hydrophobic interactions, and disulfide interactions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of low molecular sugars on the retrogradation of tapioca starch gels during storage

PubMed Central

Li, Rongfang; Kang, Huaibin; Luo, Denglin; Fan, Jinling; Zhu, Wenxue; Liu, Xinfang; Tong, Qunyi

2017-01-01

The effects of low molecular sugars (sucrose, glucose and trehalose) on the retrogradation of tapioca starch (TS) gels stored at 4°C for different periods were examined with different methods. Decrease in melting enthalpy (ΔHmelt) were obtained through differential scanning calorimetry analysis. Analysis of decrease in crystallization rate constant (k) and increase in semi-crystallization time (τ1/2) results obtained from retrogradation kinetics indicated that low molecular sugars could retard the retrogradation of TS gels and further revealed trehalose as the best inhibitor among the sugars used in this study. Fourier transform infrared (FTIR) analysis indicated that the intensity ratio of 1047 to 1022 cm−1 was increased with the addition of sugars in the order of trehalose > sucrose > glucose. Decrease in hardness parameters and increase in springiness parameters obtained from texture profile analysis (TPA) analysis also indicated that low molecular sugars could retard the retrogradation of TS gels. The results of FTIR and TPA showed a consistent sugar effect on starch retrogradation with those of DSC and retrogradation kinetics analysis. PMID:29284007

Effects of low molecular sugars on the retrogradation of tapioca starch gels during storage.

PubMed

Zhang, Xiaoyu; Li, Rongfang; Kang, Huaibin; Luo, Denglin; Fan, Jinling; Zhu, Wenxue; Liu, Xinfang; Tong, Qunyi

2017-01-01

The effects of low molecular sugars (sucrose, glucose and trehalose) on the retrogradation of tapioca starch (TS) gels stored at 4°C for different periods were examined with different methods. Decrease in melting enthalpy (ΔHmelt) were obtained through differential scanning calorimetry analysis. Analysis of decrease in crystallization rate constant (k) and increase in semi-crystallization time (τ1/2) results obtained from retrogradation kinetics indicated that low molecular sugars could retard the retrogradation of TS gels and further revealed trehalose as the best inhibitor among the sugars used in this study. Fourier transform infrared (FTIR) analysis indicated that the intensity ratio of 1047 to 1022 cm-1 was increased with the addition of sugars in the order of trehalose > sucrose > glucose. Decrease in hardness parameters and increase in springiness parameters obtained from texture profile analysis (TPA) analysis also indicated that low molecular sugars could retard the retrogradation of TS gels. The results of FTIR and TPA showed a consistent sugar effect on starch retrogradation with those of DSC and retrogradation kinetics analysis.

IMP dehydrogenase. II. Purification and properties of the enzyme from Yoshida sarcoma ascites tumor cells.

PubMed

Okada, M; Shimura, K; Shiraki, H; Nakagawa, H

1983-11-01

The preceding paper showed that IMP dehydrogenase [IMP:NAD+ oxidoreductase, EC 1.2.1.14] tended to form a precipitable complex(es) through ionic and hydrophobic interactions. On the basis of these observations, a method was developed for purification of IMP dehydrogenase from Yoshida sarcoma ascites cells. On SDS-polyacrylamide gel electrophoresis, the purified preparation (1.19 U/mg protein) appeared homogeneous and its minimum molecular weight was estimated to be 68K daltons. Amino acid analyses indicated a subunit molecular weight of 68,042. Molecular sieve chromatography in the presence of 10% (NH4)2SO4 showed that the molecular weight of the native enzyme was 127K daltons. These values indicate that the native enzyme is composed of two identical subunits. However, the purified enzyme gave 4 protein bands on polyacrylamide gel electrophoresis under non-denaturing conditions, and appeared as a single fraction in the vicinity of the void volume on Ultrogel AcA 34 column chromatography at low salt concentration, indicating that its molecular weight exceeded 200K daltons. These findings indicate that the enzyme tends to aggregate owing to its own physicochemical characteristics. The Km values for IMP and NAD were calculated to be 12 and 25 microM, respectively, and the Ki values for XMP, GMP, and AMP to be 109, 130, and 854 microM, respectively. The purified enzyme showed full activity in the presence of K+, and K+ could be partially replaced by Na+. PCMB inactivated the enzyme, but the activity was completely restored by the addition of DTT. Cl-IMP also inactivated the enzyme and IMP prevented this inactivation.(ABSTRACT TRUNCATED AT 250 WORDS)

Glycosylation site-targeted PEGylation of glucose oxidase retains native enzymatic activity.

PubMed

Ritter, Dustin W; Roberts, Jason R; McShane, Michael J

2013-04-10

Targeted PEGylation of glucose oxidase at its glycosylation sites was investigated to determine the effect on enzymatic activity, as well as the bioconjugate's potential in an optical biosensing assay. Methoxy-poly(ethylene glycol)-hydrazide (4.5kDa) was covalently coupled to periodate-oxidized glycosylation sites of glucose oxidase from Aspergillus niger. The bioconjugate was characterized using gel electrophoresis, liquid chromatography, mass spectrometry, and dynamic light scattering. Gel electrophoresis data showed that the PEGylation protocol resulted in a drastic increase (ca. 100kDa) in the apparent molecular mass of the protein subunit, with complete conversion to the bioconjugate; liquid chromatography data corroborated this large increase in molecular size. Mass spectrometry data proved that the extent of PEGylation was six poly(ethylene glycol) chains per glucose oxidase dimer. Dynamic light scattering data indicated the absence of higher-order oligomers in the PEGylated GOx sample. To assess stability, enzymatic activity assays were performed in triplicate at multiple time points over the course of 29 days in the absence of glucose, as well as before and after exposure to 5% w/v glucose for 24h. At a confidence level of 95%, the bioconjugate's performance was statistically equivalent to native glucose oxidase in terms of activity retention over the 29 day time period, as well as following the 24h glucose exposure. Finally, the bioconjugate was entrapped within a poly(2-hydroxyethyl methacrylate) hydrogel containing an oxygen-sensitive phosphor, and the construct was shown to respond approximately linearly with a 220±73% signal change (n=4, 95% confidence interval) over the physiologically-relevant glucose range (i.e., 0-400mg/dL); to our knowledge, this represents the first demonstration of PEGylated glucose oxidase incorporated into an optical biosensing assay. Copyright © 2013 Elsevier Inc. All rights reserved.

Comprehensive multiphase NMR spectroscopy: Basic experimental approaches to differentiate phases in heterogeneous samples

NASA Astrophysics Data System (ADS)

Courtier-Murias, Denis; Farooq, Hashim; Masoom, Hussain; Botana, Adolfo; Soong, Ronald; Longstaffe, James G.; Simpson, Myrna J.; Maas, Werner E.; Fey, Michael; Andrew, Brian; Struppe, Jochem; Hutchins, Howard; Krishnamurthy, Sridevi; Kumar, Rajeev; Monette, Martine; Stronks, Henry J.; Hume, Alan; Simpson, André J.

2012-04-01

Heterogeneous samples, such as soils, sediments, plants, tissues, foods and organisms, often contain liquid-, gel- and solid-like phases and it is the synergism between these phases that determine their environmental and biological properties. Studying each phase separately can perturb the sample, removing important structural information such as chemical interactions at the gel-solid interface, kinetics across boundaries and conformation in the natural state. In order to overcome these limitations a Comprehensive Multiphase-Nuclear Magnetic Resonance (CMP-NMR) probe has been developed, and is introduced here, that permits all bonds in all phases to be studied and differentiated in whole unaltered natural samples. The CMP-NMR probe is built with high power circuitry, Magic Angle Spinning (MAS), is fitted with a lock channel, pulse field gradients, and is fully susceptibility matched. Consequently, this novel NMR probe has to cover all HR-MAS aspects without compromising power handling to permit the full range of solution-, gel- and solid-state experiments available today. Using this technology, both structures and interactions can be studied independently in each phase as well as transfer/interactions between phases within a heterogeneous sample. This paper outlines some basic experimental approaches using a model heterogeneous multiphase sample containing liquid-, gel- and solid-like components in water, yielding separate 1H and 13C spectra for the different phases. In addition, 19F performance is also addressed. To illustrate the capability of 19F NMR soil samples, containing two different contaminants, are used, demonstrating a preliminary, but real-world application of this technology. This novel NMR approach possesses a great potential for the in situ study of natural samples in their native state.

Comprehensive multiphase NMR spectroscopy: basic experimental approaches to differentiate phases in heterogeneous samples.

PubMed

Courtier-Murias, Denis; Farooq, Hashim; Masoom, Hussain; Botana, Adolfo; Soong, Ronald; Longstaffe, James G; Simpson, Myrna J; Maas, Werner E; Fey, Michael; Andrew, Brian; Struppe, Jochem; Hutchins, Howard; Krishnamurthy, Sridevi; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Hume, Alan; Simpson, André J

2012-04-01

Heterogeneous samples, such as soils, sediments, plants, tissues, foods and organisms, often contain liquid-, gel- and solid-like phases and it is the synergism between these phases that determine their environmental and biological properties. Studying each phase separately can perturb the sample, removing important structural information such as chemical interactions at the gel-solid interface, kinetics across boundaries and conformation in the natural state. In order to overcome these limitations a Comprehensive Multiphase-Nuclear Magnetic Resonance (CMP-NMR) probe has been developed, and is introduced here, that permits all bonds in all phases to be studied and differentiated in whole unaltered natural samples. The CMP-NMR probe is built with high power circuitry, Magic Angle Spinning (MAS), is fitted with a lock channel, pulse field gradients, and is fully susceptibility matched. Consequently, this novel NMR probe has to cover all HR-MAS aspects without compromising power handling to permit the full range of solution-, gel- and solid-state experiments available today. Using this technology, both structures and interactions can be studied independently in each phase as well as transfer/interactions between phases within a heterogeneous sample. This paper outlines some basic experimental approaches using a model heterogeneous multiphase sample containing liquid-, gel- and solid-like components in water, yielding separate (1)H and (13)C spectra for the different phases. In addition, (19)F performance is also addressed. To illustrate the capability of (19)F NMR soil samples, containing two different contaminants, are used, demonstrating a preliminary, but real-world application of this technology. This novel NMR approach possesses a great potential for the in situ study of natural samples in their native state. Copyright © 2012 Elsevier Inc. All rights reserved.

Molecular assessment of microbiota structure and dynamics along mixed olive oil and winery wastewaters biotreatment.

PubMed

Eusébio, Ana; Tacão, Marta; Chaves, Sandra; Tenreiro, Rogério; Almeida-Vara, Elsa

2011-07-01

The major parcel of the degradation occurring along wastewater biotreatments is performed either by the native microbiota or by added microbial inocula. The main aim of this study was to apply two fingerprinting methods, temperature gradient gel electrophoresis (TGGE) and length heterogeneity-PCR (LH-PCR) analysis of 16S rRNA gene fragments, in order to assess the microbiota structure and dynamics during mixed olive oil and winery wastewaters aerobic biotreatment performed in a jet-loop reactor (JLR). Sequence homology analysis showed the presence of bacterial genera Gluconacetobacter, Klebsiella, Lactobacillus, Novosphingobium, Pseudomonas, Prevotella, Ralstonia, Sphingobium and Sphingomonas affiliated with five main phylogenetic groups: alpha-, beta- and gamma-Proteobacteria, Firmicutes and Bacteroidetes. LH-PCR analysis distinguished eight predominant DNA fragments correlated with the samples showing highest performance (COD removal rates of 67 up to 75%). Cluster analysis of both TGGE and LH-PCR fingerprinting profiles established five main clusters, with similarity coefficients higher than 79% (TGGE) and 62% (LH-PCR), and related with hydraulic retention time, indicating that this was the main factor responsible for the shifts in the microbiota structure. Canonical correspondence analysis revealed that changes observed on temperature and O(2) level were also responsible for shifts in microbiota composition. Community level metabolic profile analysis was used to test metabolic activities in samples. Integrated data revealed that the microbiota structure corresponds to bacterial groups with high degradative potential and good suitability for this type of effluents biotreatments.

An in vivo and in vitro investigation of the effect of Aloe vera gel ethanolic extract using animal model with diabetic foot ulcer

PubMed Central

Daburkar, Mohan; Lohar, Vikram; Rathore, Arvind Singh; Bhutada, Pravin; Tangadpaliwar, Shrikant

2014-01-01

Aim: To examine the preventive effect of Aloe vera gel ethanolic extract using diabetic foot ulcer (DFUs) protocol in Wistar rats. Materials and Methods: Male Wistar rats were divided into untreated control (Group I), untreated DFUs (Group II), DFUs treated with A. vera gel ethanolic extract (Group III), DFUs treated with topical A. vera gel (Group IV), DFUs treated with A. vera gel ethanolic extract and topical A. vera gel (Group V). The rats in the treatment groups were daily administered the A. vera gel and ethanolic extract for 9 days. Fasting blood glucose levels and percentage of wound ulcer contraction were measured on day 3, 6, and 9. Statistical Analysis used: The results are expressed as a mean ± Standard Error Mean (SEM). Data were analyzed using one-way analysis of variance (ANOVA) after Newman–Keuls test. P < 0.05 were considered statistically significant in all cases. Results: Oral administration of A. vera gel ethanolic extract at a dose of 300 mg/kg body weight per day to diabetic rats for a period of 9 days resulted in a significant reduction in fasting blood glucose and a significant improvement in plasma insulin. Topical application of A. vera gel at a dose 30 mg/kg body weight per day to streptozotocin (STZ)-induced diabetic rats for a period of 9 days resulted in no change in blood glucose and plasma insulin. Oral administration as well as topical application of A. vera gel ethanolic extract and gel significantly reduced the blood glucose, improved the plasma insulin, and significantly increased DNA and glycosaminoglycans (GAGs) to improve the wound ulcer healing as well as the breaking strength on day 9. Conclusions: Present findings provide a scientific rationale for the use of A. vera gel ethanolic extract, and showed that the gel attenuated the diabetic foot wound in rats. PMID:25035641

Bioactive Molecules Release and Cellular Responses of Alginate-Tricalcium Phosphate Particles Hybrid Gel

PubMed Central

Bang, Sumi; Zhang, Shengmin

2017-01-01

In this article, a hybrid gel has been developed using sodium alginate (Alg) and α-tricalcium phosphate (α-TCP) particles through ionic crosslinking process for the application in bone tissue engineering. The effects of pH and composition of the gel on osteoblast cells (MC3T3) response and bioactive molecules release have been evaluated. At first, a slurry of Alg and α-TCP has been prepared using an ultrasonicator for the homogeneous distribution of α-TCP particles in the Alg network and to achieve adequate interfacial interaction between them. After that, CaCl2 solution has been added to the slurry so that ionic crosslinked gel (Alg-α-TCP) is formed. The developed hybrid gel has been physico-chemically characterized using Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM) and a swelling study. The SEM analysis depicted the presence of α-TCP micro-particles on the surface of the hybrid gel, while cross-section images signified that the α-TCP particles are fully embedded in the porous gel network. Different % swelling ratio at pH 4, 7 and 7.4 confirmed the pH responsiveness of the Alg-α-TCP gel. The hybrid gel having lower % α-TCP particles showed higher % swelling at pH 7.4. The hybrid gel demonstrated a faster release rate of bovine serum albumin (BSA), tetracycline (TCN) and dimethyloxalylglycine (DMOG) at pH 7.4 and for the grade having lower % α-TCP particles. The MC3T3 cells are viable inside the hybrid gel, while the rate of cell proliferation is higher at pH 7.4 compared to pH 7. The in vitro cytotoxicity analysis using thiazolyl blue tetrazolium bromide (MTT), bromodeoxyuridine (BrdU) and neutral red assays ascertained that the hybrid gel is non-toxic for MC3T3 cells. The experimental results implied that the non-toxic and biocompatible Alg-α-TCP hybrid gel could be used as scaffold in bone tissue engineering. PMID:29135939

A review and meta-analysis of the enemy release hypothesis in plant–herbivorous insect systems

PubMed Central

Meijer, Kim; Schilthuizen, Menno; Beukeboom, Leo

2016-01-01

A suggested mechanism for the success of introduced non-native species is the enemy release hypothesis (ERH). Many studies have tested the predictions of the ERH using the community approach (native and non-native species studied in the same habitat) or the biogeographical approach (species studied in their native and non-native range), but results are highly variable, possibly due to large variety of study systems incorporated. We therefore focused on one specific system: plants and their herbivorous insects. We performed a systematic review and compiled a large number (68) of datasets from studies comparing herbivorous insects on native and non-native plants using the community or biogeographical approach. We performed a meta-analysis to test the predictions from the ERH for insect diversity (number of species), insect load (number of individuals) and level of herbivory for both the community and biogeographical approach. For both the community and biogeographical approach insect diversity was significantly higher on native than on non-native plants. Insect load tended to be higher on native than non-native plants at the community approach only. Herbivory was not different between native and non-native plants at the community approach, while there was too little data available for testing the biogeographical approach. Our meta-analysis generally supports the predictions from the ERH for both the community and biogeographical approach, but also shows that the outcome is importantly determined by the response measured and approach applied. So far, very few studies apply both approaches simultaneously in a reciprocal manner while this is arguably the best way for testing the ERH. PMID:28028463

Fracturing fluid cleanup by controlled release of enzymes from polyelectrolyte complex nanoparticles

NASA Astrophysics Data System (ADS)

Barati Ghahfarokhi, Reza

Guar-based polymer gels are used in the oil and gas industry to viscosify fluids used in hydraulic fracturing of production wells, in order to reduce leak-off of fluids and pressure, and improve the transport of proppants. After fracturing, the gel and associated filter cake must be degraded to very low viscosities using breakers to recover the hydraulic conductivity of the well. Enzymes are widely used to achieve this but injecting high concentrations of enzyme may result in premature degradation, or failure to gel; denaturation of enzymes at alkaline pH and high temperature conditions can also limit their applicability. In this study, application of polyelectrolyte nanoparticles for entrapping, carrying, releasing and protecting enzymes for fracturing fluids was examined. The objective of this research is to develop nano-sized carriers capable of carrying the enzymes to the filter cake, delaying the release of enzyme and protecting the enzyme against pH and temperature conditions inhospitable to native enzyme. Polyethylenimine-dextran sulfate (PEI-DS) polyelectrolyte complexes (PECs) were used to entrap two enzymes commonly used in the oil industry in order to obtain delayed release and to protect the enzyme from conditions inhospitable to native enzyme. Stability and reproducibility of PEC nanoparticles was assured over time. An activity measurement method was used to measure the entrapment efficiency of enzyme using PEC nanoparticles. This method was confirmed using a concentration measurement method (SDS-PAGE). Entrapment efficiencies of pectinase and a commercial high-temperature enzyme mixture in polyelectrolyte complex nanoparticles were maximized. Degradation, as revealed by reduction in viscoelastic moduli of borate-crosslinked hydroxypropyl guar (HPG) gel by commercial enzyme loaded in polyelectrolyte nanoparticles, was delayed, compared to equivalent systems where the enzyme mixture was not entrapped. This indicates that PEC nanoparticles delay the activity of enzymes by entrapping them. It was also observed that control PEC nanoparticles decreased both viscoelastic moduli, but with a slower rate compared to the PEC nanoparticles loaded with enzyme. Preparation shear and applied shear showed no significant effect on activity of enzyme-loaded PEC nanoparticles mixed with HPG solutions. However, fast addition of chemicals during the preparations showed smaller particle size compared to the drop-wise method. PEC nanoparticles (PECNPs) also protected both enzymes from denaturation at elevated temperature and pH. Following preparation, enzyme-loaded PEC nanoparticles were mixed with borate crosslinked HPG and the mixture was injected through a shear loop. Pectinase-loaded nanoparticles mixed with gelled HPG showed no sensitivity to shear applied along the shear loop at 25 °C. However, EL2X-loaded PEC nanoparticles showed sensitivity to shear applied along the shear loop at 40 °C. Filter cake was formed and degraded in a fluid loss cell for borate crosslinked HPG solutions mixed with either enzymes or enzyme-loaded PEC nanoparticles. Cleanup slopes of filter cake degraded using enzyme-loaded PEC nanoparticles and systems with enzymes mixed with HPG gel were significantly higher than for the filter cake formed with HPG gel mixed with no enzyme. In a different application, enzyme-loaded PEC nanoparticles showed significantly slower reduction in viscosity of HPG solution over time compared to the HPG systems mixed with enzyme. Increasing the viscosity of low concentration HPG, used as slick-water, decreases the proppant settling velocity. This is of specific interest in fracturing fluids used for unconventional reservoirs.

Isolation and functional characterization of the proenzyme form of the catalytic domains of human C1r.

PubMed Central

Lacroix, M B; Aude, C A; Arlaud, G J; Colomb, M G

1989-01-01

The proenzyme form of C1r catalytic domains was generated by limited proteolysis of native C1r with thermolysin in the presence of 4-nitrophenyl-4'-guanidinobenzoate. The final preparation, isolated by high-pressure gel permeation in the presence of 2 M-NaCl, was 70-75% proenzyme and consisted of a dimeric association of two gamma B domains, each resulting from cleavage of peptide bonds at positions 285 and 286 of C1r. Like native C1r, the isolated domains autoactivated upon incubation at 37 degrees C. Activation was inhibited by 4-nitrophenyl-4'-guanidinobenzoate but was nearly insensitive to di-isopropyl phosphorofluoridate; likewise, compared to pH 7.4, the rate of activation was decreased at pH 5.0, but was not modified at pH 10.0. In contrast, activation of the (gamma B)2 domains was totally insensitive to Ca2+. Activation of the catalytic domains, which was correlated with an irreversible increase of intrinsic fluorescence, comparable with that previously observed with native C1r [Villiers, Arlaud & Colomb (1983) Biochem. J. 215, 369-375], was reversibly inhibited at high ionic strength (2 M-NaCl), presumably through stabilization of a non-activatable conformational state. Detailed comparison of the properties of native C1r and its catalytic domains indicates that the latter contain all the structural elements that are necessary for intramolecular activation, but probably lack a regulatory mechanism associated with the N-terminal alpha beta region of C1r. Images Fig. 2. PMID:2539098

[Impact of land-use type changes on soil nitrification and ammonia-oxidizing bacterial community composition].

PubMed

Yang, Li-Lin; Mao, Ren-Zhao; Liu, Jun-Jie; Liu, Xiao-Jing

2011-11-01

A comparative study was conducted to determine nitrification potentials and ammonia-oxidizing bacterial (AOB) community composition in 0-20 cm soil depth in adjacent native forest,natural grassland, and cropland soils on the Tibetan Plateau, by incubation experiment and by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA, respectively. Cropland has the highest nitrification potential and nitrate concentration among the three land-use types (LUT), approximately 9 folds and more than 11 folds than that of the forests and grasslands, respectively. NO3(-) -N accounted for 70%-90% of inorganic N in cropland soil, while NH4(+) -N was the main form of inorganic N in forest and grassland soils. Nitrification potentials and nitrate concentrations showed no significant difference between native forest and grassland soils. The native forest showed the lowest nitrification potentials and the lowest AOB diversity and community composition among the three LUT. Conversions from natural grasslands to croplands remarkably decreased the AOB diversity and composition, but croplands remain high similarity in AOB community composition compared with grasslands. The minimal and the lowest diversity of AOB in native forests directly resulted to the lowest nitrification potentials compared to natural grasslands and croplands. From the fact of the highest nitrification potentials and nitrate concentrations in croplands indicated that there were the most substantial AOB with higher activity and priority. The results provide evidence that changes of land-use type can affect both soil nitrogen internal cycling process, the diversity, community and activity of AOB, which further affect soil environment quality and the long-term sustainability of ecosystems.

Comparative Testis Tissue Proteomics Using 2-Dye Versus 3-Dye DIGE Analysis.

PubMed

Holland, Ashling

2018-01-01

Comparative tissue proteomics aims to analyze alterations of the proteome in response to a stimulus. Two-dimensional difference gel electrophoresis (2D-DIGE) is a modified and advanced form of 2D gel electrophoresis. DIGE is a powerful biochemical method that compares two or three protein samples on the same analytical gel, and can be used to establish differentially expressed protein levels between healthy normal and diseased pathological tissue sample groups. Minimal DIGE labeling can be used via a 2-dye system with Cy3 and Cy5 or a 3-dye system with Cy2, Cy3, and Cy5 to fluorescently label samples with CyDye flours pre-electrophoresis. DIGE circumvents gel-to-gel variability by multiplexing samples to a single gel and through the use of a pooled internal standard for normalization. This form of quantitative high-resolution proteomics facilitates the comparative analysis and evaluation of tissue protein compositions. Comparing tissue groups under different conditions is crucially important for advancing the biomedical field by characterization of cellular processes, understanding pathophysiological development and tissue biomarker discovery. This chapter discusses 2D-DIGE as a comparative tissue proteomic technique and describes in detail the experimental steps required for comparative proteomic analysis employing both options of 2-dye and 3-dye DIGE minimal labeling.

Self-assembling Structures and Sol-Gel Transition of Optically Active and Racemic 12-Hydroxystearic Acids in Organic Solvents

NASA Astrophysics Data System (ADS)

Takeno, Hiroyuki; Mochizuki, Tomomitsu; Yoshiba, Kazuto; Kondo, Shingo; Dobashi, Toshiaki

Self-assembling structures and sol-gel transition in solution of optically active and racemic 12-Hydroxystearic acids (HSA) have been investigated by means of small-angle X-ray scattering (SAXS), differential scanning calorimetry and rheological measurements. Apparently two kinds of gel, transparent gel and turbid gel were obtained in different solvents or by changing concentrations in the same solvent. The melting temperature of the turbid gel is higher than that of the transparent gel. The difference can be qualitatively explained by the dissolution of the crystals (melting point depression) in non-ideal solutions. The SAXS profiles of the transparent gel composed of fibrillar structures have a similar shape at different concentrations, although the intensity is larger for the gels with higher concentrations of 12-HSA. The SAXS analysis reveals that the cross-section of fibrils have square or circular shape (no anisotropic shape) with the radius of gyration 83 Å. On the other hand, for the turbid gel structural inhomnogeneity becomes significant with concentration. The gelation properties and the structures are found to be similar in the racemic HSA gel and the optically active (D-HSA) gel.

Anisotropic Mechanical Properties of Magnetically Aligned Fibrin Gels Measured by Magnetic Resonance Elastography

PubMed Central

Namani, Ravi; Wood, Matthew D.; Sakiyama-Elbert, Shelly E.; Bayly, Philip V.

2009-01-01

The anisotropic mechanical properties of magnetically aligned fibrin gels were measured by magnetic resonance elastography (MRE) and by a standard mechanical test: unconfined compression. Soft anisotropic biomaterials are notoriously difficult to characterize, especially in vivo. MRE is well-suited for efficient, non-invasive, and nondestructive assessment of shear modulus. Direction-dependent differences in shear modulus were found to be statistically significant for gels polymerized at magnetic fields of 11.7T and 4.7T compared to control gels. Mechanical anisotropy was greater in the gels polymerized at the higher magnetic field. These observations were consistent with results from unconfined compression tests. Analysis of confocal microscopy images of gels showed measurable alignment of fibrils in gels polymerized at 11.7T. This study provides direct, quantitative measurements of the anisotropy in mechanical properties that accompanies fibril alignment in fibrin gels. PMID:19656516

Mechanics and crack formation in the extracellular matrix with articular cartilage as a model system

NASA Astrophysics Data System (ADS)

Kearns, Sarah; Silverberg, Jesse; Bonassar, Lawrence; Cohen, Itai; Das, Moumita

We investigate the mechanical structure-function relations in the extracellular matrix (ECM) with focus on crack formation and failure. As a model system, our study focuses on the ECM in articular cartilage (AC), the tissue that covers the ends of bones, and distributes load in joints including in the knees, shoulders, and hips. The strength, toughness, and crack resistance of native articular cartilage is unparalleled in materials made by humankind. This mechanical response is mainly due to its ECM. The ECM in AC has two major mechanobiological components: a network of the biopolymer collagen and a flexible aggrecan gel. We model this system as a biopolymer network embedded in a swelling gel, and investigate the conditions for the formation and propagation of cracks using a combination of rigidity percolation theory and energy minimization approaches. Our results may provide useful insights into the design principles of the ECM as well as of biomimetic hydrogels that are mechanically robust and can, at the same time, easily adapt to cues in their surroundings. This work was partially supported by a Cottrell College Science Award.

Evaluation of capillary zone electrophoresis for the determination of protein composition in therapeutic immunoglobulins and human albumins.

PubMed

Christians, Stefan; van Treel, Nadine Denise; Bieniara, Gabriele; Eulig-Wien, Annika; Hanschmann, Kay-Martin; Giess, Siegfried

2016-07-01

Capillary zone electrophoresis (CZE) provides an alternative means of separating native proteins on the basis of their inherent electrophoretic mobilities. The major advantage of CZE is the quantification by UV detection, circumventing the drawbacks of staining and densitometry in the case of gel electrophoresis methods. The data of this validation study showed that CZE is a reliable assay for the determination of protein composition in therapeutic preparations of human albumin and human polyclonal immunoglobulins. Data obtained by CZE are in line with "historical" data obtained by the compendial method, provided that peak integration is performed without time correction. The focus here was to establish a rapid and reliable test to substitute the current gel based zone electrophoresis techniques for the control of protein composition of human immunoglobulins or albumins in the European Pharmacopoeia. We believe that the more advanced and modern CZE method described here is a very good alternative to the procedures currently described in the relevant monographs. Copyright © 2016 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Changes of Template Activity and Proteins of Chromatin during Wheat Germination

PubMed Central

Yoshida, Kouichi; Sasaki, Kimiko

1977-01-01

Relationships between changes in template activity and composition of chromatin during germination of wheat embyros (Triticum aestivum L.) were investigated. The template activity of chromatin was determined with exogenous DNA-dependent RNA polymerase II (EC 2.7.7.6) prepared from wheat embryos. It was essentially constant for 18 hours of germination, corresponding to 2.5% of that of a native calf thymus DNA. Thereafter, the activity increased 2-fold and 5-fold at 24 and 60 hours of germination, respectively. Chromatin-associated proteins were separated into at least 22 distinct bands by sodium dodecyl sulfate gel electrophoresis throughout 60 hours of germination. Significant changes were observed in two nonhistone proteins, approximate molecular weights 59,000 and 39,000: the amount of the former was constant up to 18 hours, reduced for the period from 18 to 60 hours, and that of the latter was decreased for the period from 18 to 60 hours of germination. No change was observed in the number of histone components by acid-urea gel electrophoresis. Images PMID:16659879

The pPSU Plasmids for Generating DNA Molecular Weight Markers.

PubMed

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

2017-05-26

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

Purification and biochemical characterization of methionine aminopeptidase (MetAP) from Mycobacterium smegmatis mc2155.

PubMed

Narayanan, Sai Shyam; Ramanujan, Ajeena; Krishna, Shyam; Nampoothiri, Kesavan Madhavan

2008-12-01

The methionine aminopeptidase (MetAP) catalyzes the removal of amino terminal methionine from newly synthesized polypeptide. MetAP from Mycobacterium smegmatis mc(2) 155 was purified from the culture lysate in four sequential steps to obtain a final purification fold of 22. The purified enzyme exhibited a molecular weight of approximately 37 kDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Activity staining was performed to detect the methionine aminopeptidase activity on native polyacrylamide gel. The enzyme was characterized biochemically, using L-methionine p-nitroanilide as substrate. The enzyme was found to have a temperature and pH optimum of 50 degrees C and 8.5, respectively, and was found to be stable at 50 degrees C with half-life more than 8 h. The enzyme activity was enhanced by Mg(2+) and Co(2+) and was inhibited by Fe(2+) and Cu(2+). The enzyme activity inhibited by EDTA is restored in presence of Mg(2+) suggesting the possible role of Mg(2+) as metal cofactor of the enzyme in vitro.

Properties of purified cytosolic isoenzyme I of Cu,Zn-superoxide dismutase from Nicotiana plumbaginifolia leaves.

PubMed

Ragusa, S; Cambria, M T; Scarpa, M; Di Paolo, M L; Falconi, M; Rigo, A; Cambria, A

2001-11-01

The isoenzyme I of cytosolic Cu,Zn-superoxide dismutase (SOD) from Nicotiana plumbaginifolia (tobacco) leaves has been purified to apparent homogeneity. The relative molecular mass of the native isoenzyme, determined by gel filtration chromatography, is about 33.2 kDa. SDS-polyacrylamide gel electrophoresis shows that the enzyme is composed of two equal subunits of 16.6 kDa The isolectric point, assayed by isoelectric focusing, in the pH range of 3.5-6.5, is 4.3. The enzyme stability was tested at different temperatures, pH, and concentration of inhibitors (KCN and H(2)O(2)). The catalytic constant (k(cat)) was 1.17 +/- 0.14 x 10(9) M(-1) s(-1) at pH 9.9 and 0.1 M ionic strength. The activation energy of the thermal denaturation process is 263 kJ mol(-1). The electrostatic surface potential of the modeled tobacco Cu,Zn-SOD I was calculated showing that the functional spatial network of charges on the protein surface has been maintained, independently of the amino acid substitution around the active sites. Copyright 2001 Academic Press.

Statistical analysis of native contact formation in the folding of designed model proteins

NASA Astrophysics Data System (ADS)

Tiana, Guido; Broglia, Ricardo A.

2001-02-01

The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge: (a) local, fast forming highly stable native bonds built by some of the most strongly interacting amino acids of the protein; (b) nonlocal bonds formed late in the folding process, in coincidence with the folding nucleus, and involving essentially the same strongly interacting amino acids already participating in the fast bonds; (c) the rest of the native bonds whose behavior is subordinated, to a large extent, to that of the strong local and nonlocal native contacts.

Silk Electrogel Based Gastroretentive Drug Delivery System

NASA Astrophysics Data System (ADS)

Wang, Qianrui

Gastric cancer has become a global pandemic and there is imperative to develop efficient therapies. Oral dosing strategy is the preferred route to deliver drugs for treating the disease. Recent studies suggested silk electro hydrogel, which is pH sensitive and reversible, has potential as a vehicle to deliver the drug in the stomach environment. The aim of this study is to establish in vitro electrogelation e-gel based silk gel as a gastroretentive drug delivery system. We successfully extended the duration of silk e-gel in artificial gastric juice by mixing silk solution with glycerol at different ratios before the electrogelation. Structural analysis indicated the extended duration was due to the change of beta sheet content. The glycerol mixed silk e-gel had good doxorubicin loading capability and could release doxorubicin in a sustained-release profile. Doxorubicin loaded silk e-gels were applied to human gastric cancer cells. Significant cell viability decrease was observed. We believe that with further characterization as well as functional analysis, the silk e-gel system has the potential to become an effective vehicle for gastric drug delivery applications.

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

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

Ono, K; Fujimoto, S; Akagi, Y

2014-06-01

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

Purification and chemical characterisation of a cell wall-associated β-galactosidase from mature sweet cherry (Prunus avium L.) fruit.

PubMed

Gerardi, Carmela; Blando, Federica; Santino, Angelo

2012-12-01

Using four different chromatographic steps, β-galactosidase was purified from the ripe fruit of sweet cherry to apparent electrophoretic homogeneity with approximately 131-fold purification. The Prunus avium β-galactosidase showed an apparent molecular mass of about 100 kDa and consisted of four different active polypeptides with pIs of about 7.9, 7.4, 6.9 and 6.4 as estimated by native IEF and β-galactosidase-activity staining. The active polypeptides were individually excised from the gel and subjected to SDS-PAGE. Each of the four native enzymes showing β-galactosidase activity was composed of two polypeptides with an estimated mass of 54 and 33 kDa. Both of these polypeptides were subjected to N-terminal amino acid sequence analysis. The 54 kDa polypeptide of sweet cherry β-galactosidase showed a 43% identity with the 44 kDa subunit of persimmon and apple β-galactosidases and the 48 kDa subunit of carambola galactosidase I. The sweet cherry β-galactosidase exhibited a strict specificity towards p-nitrophenyl β-D-galactopyranoside, a pH optimum of 4.0 and K(m) and V(max) values of 0.42 mM and 4.12 mmol min(-1) mg(-1) of protein respectively with this substrate. The enzyme was also active towards complex glycans. Taken together the results of this study prompted a role for this class of enzymes on sweet cherry fruit ripening and softening. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Properties and mutation studies of a bacteriophage-derived chimeric recombinant staphylolytic protein P128

PubMed Central

Saravanan, Sanjeev Rajagopalan; Paul, Vivek Daniel; George, Shilpa; Sundarrajan, Sudarson; Kumar, Nirmal; Hebbur, Madhavi; Kumar, Naveen; Veena, Ananda; Maheshwari, Uma; Appaiah, Chemira Biddappa; Chidambaran, Muralidharan; Bhat, Anuradha Gopal; Hariharan, Sukumar; Padmanabhan, Sriram

2013-01-01

P128 is a chimeric anti-staphylococcal protein having a catalytic domain from a Staphylococcus bacteriophage K tail associated structural protein and a cell wall targeting domain from the Staphylococcus bacteriocin-lysostaphin. In this study, we disclose additional properties of P128 and compared the same with lysostaphin. While lysostaphin was found to get inactivated by heat and was inactive on its parent strain S. simulans biovar staphylolyticus, P128 was thermostable and was lytic towards S. simulans biovar staphylolyticus demonstrating a difference in their mechanism of action. Selected mutation studies of the catalytic domain of P128 showed that arginine and cysteine, at 40th and 76th positions respectively, are critical for the staphylolytic activity of P128, although these amino acids are not conserved residues. In comparison to native P128, only the R40S mutant (P301) was catalytically active on zymogram gel and had a similar secondary structure, as assessed by circular dichroism analysis and in silico modeling with similar cell binding properties. Mutation of the arginine residue at 40th position of the P128 molecule caused dramatic reduction in the Vmax (∆OD600 [mg/min]) value (nearly 270 fold) and the recombinant lysostaphin also showed lesser Vmax value (nearly 1.5 fold) in comparison to the unmodified P128 protein. The kinetic parameters such as apparent Km (Km APP) and apparent Kcat (KcatAPP) of the native P128 protein also showed significant differences in comparison to the values observed for P301 and lysostaphin. PMID:24251076

Physical and anti-microbial characteristics of carbon nanoparticles prepared from lamp soot

NASA Astrophysics Data System (ADS)

Mohanty, B.; Verma, Anita K.; Claesson, P.; Bohidar, H. B.

2007-11-01

Soot originating from the burning of butter and mustard oil in a lamp with a cotton wick was collected on a brass plate and dispersed in water and carbon tetrachloride (CCl4) as naked, and as Gum Arabic (GA, a anionic polyelectrolyte)-coated nanoparticles in water. They were physically characterized, and their anti-bacterial activities were probed on gram positive and negative bacterial colonies. TEM data revealed the presence of 35-55 nm diameter spherical carbon nanoparticles in water and CCl4. The dynamic light scattering determined the average hydrodynamic diameter for the same samples, which was found to be ≈100 nm (in CCl4) and ≈240 nm (in water), implying the packing of these nanoparticles into clusters. GA-coated particles yielded stable suspensions in water, but the clusters were almost the same in size (≈250 nm). The zeta potential distributions of the naked and the GA-coated nanoparticles were found to be unimodal and bimodal, respectively, with both yielding mean zeta potential values nearly equal to zero. Results of energy-dispersive x-ray analysis (EDAX) confirmed the absence of toxic metallic elements inside the specimen. X-ray diffraction study confirmed the presence of amorphous as well as graphitized carbon in these nanostructures. The anti-microbial activities in terms of growth inhibition for the carbon nanoparticles against Staphylococcus aureus, ATCC 13709 (native strain) and Klebsiella pneumonia ATCC 29655 (native strain) were assayed in agar gel. In vitro testing revealed significant anti-microbial activity against Klebsiella pneumonia, but carbon nanoparticles were unable to kill Staphylococcus aureus.

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

PubMed

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

2016-08-01

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

Conformational changes in human Hsp70 induced by high hydrostatic pressure produce oligomers with ATPase activity but without chaperone activity.

PubMed

Araujo, Thaís L S; Borges, Julio Cesar; Ramos, Carlos H; Meyer-Fernandes, José Roberto; Oliveira Júnior, Reinaldo S; Pascutti, Pedro G; Foguel, Debora; Palhano, Fernando L

2014-05-13

We investigated the folding of the 70 kDa human cytosolic inducible protein (Hsp70) in vitro using high hydrostatic pressure as a denaturing agent. We followed the structural changes in Hsp70 induced by high hydrostatic pressure using tryptophan fluorescence, molecular dynamics, circular dichroism, high-performance liquid chromatography gel filtration, dynamic light scattering, ATPase activity, and chaperone activity. Although monomeric, Hsp70 is very sensitive to hydrostatic pressure; after pressure had been removed, the protein did not return to its native sate but instead formed oligomeric species that lost chaperone activity but retained ATPase activity.

Electroactive polymer gels based on epoxy resin

NASA Astrophysics Data System (ADS)

Samui, A. B.; Jayakumar, S.; Jayalakshmi, C. G.; Pandey, K.; Sivaraman, P.

2007-04-01

Five types of epoxy gels have been synthesized from common epoxy resins and hardeners. Fumed silica and nanoclay, respectively, were used as fillers and butyl methacrylate/acrylamide were used as monomer(s) for making interpenetrating polymer networks (IPNs) in three compositions. Swelling study, tensile property evaluation, dynamic mechanical thermal analysis, thermo-gravimetric analysis, scanning electron microscopy and electroactive property evaluation were done. The gels have sufficient mechanical strength and the time taken for bending to 20° was found to be 22 min for forward bias whereas it was just 12 min for reverse bias.

Gelatin modified lipid nanoparticles for anti- viral drug delivery.

PubMed

K S, Joshy; S, Snigdha; Kalarikkal, Nandakumar; Pothen, Laly A; Thomas, Sabu

2017-10-01

The major challenges to clinical application of zidovudine are its moderate aqueous solubility and relative short half-life and serious side effects due to frequent administrations. We investigated the preparation of zidovudine-loaded nanoparticles based on lipids which were further modified with the polymer gelatin. Formulation and stability of the modified nanoparticles were analysed from the physico-chemical characterizations. The interactions of nanoparticles with blood components were tested by haemolysis and aggregation studies. The drug content and entrapment efficiencies were assessed by UV analysis. The effect of nanoparticles on protein adsorption was assessed by native polyacrylamide gel electrophoresis (PAGE). In vitro release studies showed a sustained release profile of zidovudine. In vitro cytotoxicity and cellular uptake of the zidovudine-loaded nanoparticles were performed in MCF-7 and neuro 2a brain cells. The enhanced cellular internalization of drug loaded modified nanoparticles in both the cell lines were revealed by fluorescence microscopy. Hence the present study focuses on the feasibility of zidovudine-loaded polymer modified lipid nanoparticles as carriers for safe and efficient HIV/AIDS therapy. Copyright © 2017 Elsevier B.V. All rights reserved.

MAMP (microbe-associated molecular pattern)-induced changes in plasma membrane-associated proteins.

PubMed

Uhlíková, Hana; Solanský, Martin; Hrdinová, Vendula; Šedo, Ondrej; Kašparovský, Tomáš; Hejátko, Jan; Lochman, Jan

2017-03-01

Plant plasma membrane associated proteins play significant roles in Microbe-Associated Molecular Pattern (MAMP) mediated defence responses including signal transduction, membrane transport or energetic metabolism. To elucidate the dynamics of proteins associated with plasma membrane in response to cryptogein, a well-known MAMP of defence reaction secreted by the oomycete Phytophthora cryptogea, 2D-Blue Native/SDS gel electrophoresis of plasma membrane fractions was employed. This approach revealed 21 up- or down-regulated protein spots of which 15 were successfully identified as proteins related to transport through plasma membrane, vesicle trafficking, and metabolic enzymes including cytosolic NADP-malic enzyme and glutamine synthetase. Observed changes in proteins were also confirmed on transcriptional level by qRT-PCR analysis. In addition, a significantly decreased accumulation of transcripts observed after employment of a mutant variant of cryptogein Leu41Phe, exhibiting a conspicuous defect in induction of resistance, sustains the contribution of identified proteins in cryptogein-triggered cellular responses. Our data provide further evidence for dynamic MAMP-induced changes in plasma membrane associated proteins. Copyright © 2016 Elsevier GmbH. All rights reserved.

Resistance of human butyrylcholinesterase to methylene blue-catalyzed photoinactivation; mass spectrometry analysis of oxidation products.

PubMed

Tacal, Ozden; Li, Bin; Lockridge, Oksana; Schopfer, Lawrence M

2013-01-01

Methylene blue, 3, 7-bis(dimethylamino)-phenothiazin-5-ium chloride, is a reversible inhibitor of human butyrylcholinesterase (BChE) in the absence of light. In the presence of light and oxygen, methylene blue promotes irreversible inhibition of human BChE as a function of time, requiring 3 h irradiation to inhibit 95% activity. Inactivation was accompanied by a progressive loss of Coomassie-stained protein bands on native and denaturing polyacrylamide gels, suggesting backbone fragmentation. Aggregation was not detected. MALDI-TOF/TOF mass spectrometry identified oxidized tryptophan (W52, 56, 231, 376, 412, 490, 522), oxidized methionine (M81, 144, 302, 532, 554, 555), oxidized histidine (H214), oxidized proline (P230), oxidized cysteine (C519) and oxidized serine (S215). A 20 min irradiation in the presence of methylene blue resulted in 17% loss of BChE activity, suggesting that BChE is relatively resistant to methylene blue-catalyzed photoinactivation and that therefore this process could be used to sterilize BChE preparations. © 2012 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2012 The American Society of Photobiology.

Cloning and polymorphisms of yak lactate dehydrogenase B gene.

PubMed

Wang, Guosheng; Zhao, Xingbo; Zhong, Juming; Cao, Meng; He, Qinghua; Liu, Zhengxin; Lin, Yaqiu; Xu, Yaou; Zheng, Yucai

2013-06-05

The main objective of this work was to study the unique polymorphisms of the lactate dehydrogenase-1 (LDH1) gene in yak (Bos grunniens). Native polyacrylamide gel electrophoresis revealed three phenotypes of LDH1 (a tetramer of H subunit) in yak heart and longissimus muscle extracts. The corresponding gene, ldhb, encoding H subunits of three LDH1 phenotypes was obtained by RT-PCR. A total of six nucleotide differences were detected in yak ldhb compared with that of cattle, of which five mutations cause amino acid substitutions. Sequence analysis shows that the G896A and C689A, mutations of ldhb gene, result in alterations of differently charged amino acids, and create the three phenotypes (F, M, and S) of yak LDH1. Molecular modeling of the H subunit of LDH indicates that the substituted amino acids are not located within NAD+ or substrate binding sites. PCR-RFLP examination of G896A mutation demonstrated that most LDH1-F samples are actually heterozygote at this site. These results help to elucidate the molecular basis and genetic characteristic of the three unique LDH1 phenotypes in yak.

Cloning and Polymorphisms of Yak Lactate Dehydrogenase b Gene

PubMed Central

Wang, Guosheng; Zhao, Xingbo; Zhong, Juming; Cao, Meng; He, Qinghua; Liu, Zhengxin; Lin, Yaqiu; Xu, Yaou; Zheng, Yucai

2013-01-01

The main objective of this work was to study the unique polymorphisms of the lactate dehydrogenase-1 (LDH1) gene in yak (Bos grunniens). Native polyacrylamide gel electrophoresis revealed three phenotypes of LDH1 (a tetramer of H subunit) in yak heart and longissimus muscle extracts. The corresponding gene, ldhb, encoding H subunits of three LDH1 phenotypes was obtained by RT-PCR. A total of six nucleotide differences were detected in yak ldhb compared with that of cattle, of which five mutations cause amino acid substitutions. Sequence analysis shows that the G896A and C689A, mutations of ldhb gene, result in alterations of differently charged amino acids, and create the three phenotypes (F, M, and S) of yak LDH1. Molecular modeling of the H subunit of LDH indicates that the substituted amino acids are not located within NAD+ or substrate binding sites. PCR-RFLP examination of G896A mutation demonstrated that most LDH1-F samples are actually heterozygote at this site. These results help to elucidate the molecular basis and genetic characteristic of the three unique LDH1 phenotypes in yak. PMID:23739677

Purification of a PHA-like chitin-binding protein from Acacia farnesiana seeds: a time-dependent oligomerization protein.

PubMed

Santi-Gadelha, T; Rocha, B A M; Oliveira, C C; Aragão, K S; Marinho, E S; Gadelha, C A A; Toyama, M H; Pinto, V P T; Nagano, C S; Delatorre, P; Martins, J L; Galvani, F R; Sampaio, A H; Debray, H; Cavada, B S

2008-07-01

A lectin-like protein from the seeds of Acacia farnesiana was isolated from the albumin fraction, characterized, and sequenced by tandem mass spectrometry. The albumin fraction was extracted with 0.5 M NaCl, and the lectin-like protein of A. farnesiana (AFAL) was purified by ion-exchange chromatography (Mono-Q) followed by chromatofocusing. AFAL agglutinated rabbit erythrocytes and did not agglutinate human ABO erythrocytes either native or treated with proteolytic enzymes. In sodium dodecyl sulfate gel electrophoresis under reducing and nonreducing conditions, AFAL separated into two bands with a subunit molecular mass of 35 and 50 kDa. The homogeneity of purified protein was confirmed by chromatofocusing with a pI = 4.0 +/- 0.5. Molecular exclusion chromatography confirmed time-dependent oligomerization in AFAL, in accordance with mass spectrometry analysis, which confers an alteration in AFAL affinity for chitin. The protein sequence was obtained by a liquid chromatography quadrupole time-of-flight experiment and showed that AFAL has 68% and 63% sequence similarity with lectins of Phaseolus vulgaris and Dolichos biflorus, respectively.

Saccharification efficiencies of multi-enzyme complexes produced by aerobic fungi.

PubMed

Badhan, Ajay; Huang, Jiangli; Wang, Yuxi; Abbott, D Wade; Di Falco, Marcos; Tsang, Adrian; McAllister, Tim

2018-05-24

In the present study, we have characterized high molecular weight multi-enzyme complexes in two commercial enzymes produced by Trichoderma reesei (Spezyme CP) and Penicillium funiculosum (Accellerase XC). We successfully identified 146-1000 kDa complexes using Blue native polyacrylamide gel electrophoresis (BN-PAGE) to fractionate the protein profile in both preparations. Identified complexes dissociated into lower molecular weight constituents when loaded on SDS PAGE. Unfolding of the secondary structure of multi-enzyme complexes with trimethylamine (pH >10) suggested that they were not a result of unspecific protein aggregation. Cellulase (CMCase) profiles of extracts of BN-PAGE fractionated protein bands confirmed cellulase activity within the multi-enzyme complexes. A microassay was used to identify protein bands that promoted high levels of glucose release from barley straw. Those with high saccharification yield were subjected to LC-MS analysis to identify the principal enzymatic activities responsible. The results suggest that secretion of proteins by aerobic fungi leads to the formation of high molecular weight multi-enzyme complexes that display activity against carboxymethyl cellulose and barley straw. Copyright © 2018. Published by Elsevier B.V.

Nearly Finished Genomes Produced Using Gel Microdroplet Culturing (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

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

Fitzsimmons, Michael

2012-06-01

Michael Fitzsimmons from Los Alamos National Laboratory gives a talk titled "Nearly Finished Genomes Produced Using Gel Microdroplet Culturing" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Nearly Finished Genomes Produced Using Gel Microdroplet Culturing (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Fitzsimmons, Michael

2018-01-22

Michael Fitzsimmons from Los Alamos National Laboratory gives a talk titled "Nearly Finished Genomes Produced Using Gel Microdroplet Culturing" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Corrosion of iron by iodide-oxidizing bacteria isolated from brine in an iodine production facility.

PubMed

Wakai, Satoshi; Ito, Kimio; Iino, Takao; Tomoe, Yasuyoshi; Mori, Koji; Harayama, Shigeaki

2014-10-01

Elemental iodine is produced in Japan from underground brine (fossil salt water). Carbon steel pipes in an iodine production facility at Chiba, Japan, for brine conveyance were found to corrode more rapidly than those in other facilities. The corroding activity of iodide-containing brine from the facility was examined by immersing carbon steel coupons in "native" and "filter-sterilized" brine samples. The dissolution of iron from the coupons immersed in native brine was threefold to fourfold higher than that in the filter-sterilized brine. Denaturing gradient gel electrophoresis analyses revealed that iodide-oxidizing bacteria (IOBs) were predominant in the coupon-containing native brine samples. IOBs were also detected in a corrosion deposit on the inner surface of a corroded pipe. These results strongly suggested the involvement of IOBs in the corrosion of the carbon steel pipes. Of the six bacterial strains isolated from a brine sample, four were capable of oxidizing iodide ion (I(-)) into molecular iodine (I(2)), and these strains were further phylogenetically classified into two groups. The iron-corroding activity of each of the isolates from the two groups was examined. Both strains corroded iron in the presence of potassium iodide in a concentration-dependent manner. This is the first report providing direct evidence that IOBs are involved in iron corrosion. Further, possible mechanisms by which IOBs corrode iron are discussed.

Chia (Salvia hispanica L) gel can be used as egg or oil replacer in cake formulations.

PubMed

Borneo, Rafael; Aguirre, Alicia; León, Alberto E

2010-06-01

This study determined the overall acceptability, sensory characteristics, functional properties, and nutrient content of cakes made using chia (Salvia hispanica L) gel as a replacement for oil or eggs. Chia gel was used to replace 25%, 50%, and 75% of oil or eggs in a control cake formulation. Seventy-five untrained panelists participated in rating cakes on a seven-point hedonic scale. Analysis of variance conducted on the sensory characteristics and overall acceptability indicated a statistically significant effect when replacing oil or eggs for color, taste, texture, and overall acceptability (P<0.05). Post hoc analysis (using Fisher's least significant difference method) indicated that the 25% chia gel cakes were not significantly different from the control for color, taste, texture, and overall acceptability. The 50% oil substituted (with chia gel) cake, compared to control, had 36 fewer kilocalories and 4 g less fat per 100-g portion. Cake weight was not affected by chia gel in the formulation, although cake volume was lower as the percentage of substitution increased. Symmetry was generally not affected. This study demonstrates that chia gel can replace as much as 25% of oil or eggs in cakes while yielding a more nutritious product with acceptable sensory characteristics. 2010 American Dietetic Association. Published by Elsevier Inc. All rights reserved.

Simultaneous UPLC-MS/MS analysis of native catechins and procyanidins and their microbial metabolites in intestinal contents and tissues of male Wistar Furth inbred rats.

PubMed

Goodrich, Katheryn M; Neilson, Andrew P

2014-05-01

Procyanidins have been extensively investigated for their potential health protective activities. However, the potential bioactivities of procyanidins are limited by their poor bioavailability. The majority of the ingested dose remains unabsorbed and reaches the colon where extensive microbial metabolism occurs. Most existing analytical methods measure either native compounds (catechins and procyanidins), or their microbial metabolites. The objectives of this study were to develop a high-throughput extraction and UPLC-MS/MS method for simultaneous measurement of both native procyanidins and their metabolites, facilitating high-throughput analysis of native and metabolite profiles in various regions of the colon. The present UPLC-MS/MS method facilitates simultaneous resolution and detection of authentic standards of 14 native catechin monomers and procyanidins, as well as 24 microbial metabolites. Detection and resolution of an additional 3 procyanidin dimers and 10 metabolites for which standards were not available was achieved. Elution and adequate resolution of both native compounds and metabolites were achieved within 10min. The intraday repeatability for native compounds was between 1.1 and 16.5%, and the interday repeatability for native compounds was between 2.2 and 25%. Intraday and interday repeatability for metabolites was between 0.6 and 24.1% and 1 and 23.9%, respectively. Observed lower limits of quantification for native compounds were ∼9-350fmol on-column, and for the microbial metabolites were ∼0.8-12,000fmol on-column. Observed lower limits of detection for native compounds were ∼4.5-190fmol on-column, and for metabolites were 0.304-6020fmol on-column. For native monomers and procyanidins, extraction recoveries ranged from 38 to 102%. Extraction recoveries for the 9 microbial metabolites tested ranged from 41 to 95%. Data from tissue analysis of rats gavaged with grape seed extract indicate fairly high accumulation of native compounds, primarily monomers and dimers, in the cecum and colon. Metabolite data indicate the progressive nature of microbial metabolism as the digesta moves through the lower GI tract. This method facilitates the high-throughput, sensitive, and simultaneous analysis of both native compounds and their microbial metabolites in biological samples and provides a more efficient means of extraction and analysis than previous methods. Copyright © 2014 Elsevier B.V. All rights reserved.

Gelling Properties of Fish/Pork Mince Mixtures.

PubMed

Liu, Ru; Zhao, Siming; Regenstein, Joe M; Liu, Qing; Yang, Hong; Xiong, Shanbai

2016-02-01

The gel properties of silver carp/pork mince mixtures were investigated as well as the protein structural changes and interactions during gelling using rheology, SEM, and FT-Raman spectroscopy. The breaking force values for gels containing 0% to 40% pork was significantly lower (P < 0.05) compared with gels containing 50% to 100% pork. Gels containing 70% to 100% pork had significantly higher (P < 0.05) breaking force values compared with gels containing 50% to 60% pork. Deformation values were more mixed. Dynamic rheological data suggested that mixing fish and pork at 3:7 could strengthen the gel network. The addition of 40% pork or above, significantly decreased (P < 0.05) the water retention of the gels compared with the 100% fish gels. The dimensional ordering of gels was also reduced by addition of pork. The reduced ordering was one of the reasons for the low water retention for fish/pork mixed gels. Raman spectral analysis confirmed that mixing fish and pork in 7:3 and 3:7 ratios could promote hydrophobic interactions such as bringing tyrosine residues into the intermolecular interface. The interactions in the 3:7 fish/pork mixed gels were favorable for forming a stronger gel. However, the interactions in the 7:3 fish/pork mixed gels were adverse. The water retention of gels was related to both molecular interactions and secondary structures of protein as well as the microstructure of the gels. © 2016 Institute of Food Technologists®

Molecular Analysis of Bacterial Community Dynamics During Bioaugmentation Studies in a Soil Column and at a Field Test Site

DTIC Science & Technology

2004-06-03

82 4.14 A GelComparII-generated UPGMA clustering dendrogram and corresponding normalized restriction...A GelComparII-generated UPGMA clustering dendrogram and corresponding normalized restriction profiles from the community...A GelComparII-generated UPGMA clustering dendrogram and corresponding normalized restriction profiles from the community

Coupled gel spreading and diffusive transport models describing microbicidal drug delivery

NASA Astrophysics Data System (ADS)

Funke, Claire; MacMillan, Kelsey; Ham, Anthony S.; Szeri, Andrew J.; Katz, David F.

2016-11-01

Gels are a drug delivery platform being evaluated for application of active pharmaceutical ingredients, termed microbicides, that act topically against infection by sexually transmitted HIV. Despite success in one Phase IIb trial of a vaginal gel delivering tenofovir, problems of user adherence to designed gel application regimen compromised results in two other trials. The microbicide field is responding to this issue by simultaneously analyzing behavioral determinants of adherence and pharmacological determinants of drug delivery. Central to both user adherence and mucosal drug delivery are gel properties (e.g. rheology) and applied volume. The specific problem to be solved here is to develop a model for how gel rheology and volume, interacting with loaded drug concentration, govern the transport of the microbicide drug tenofovir into the vaginal mucosa to its stromal layer. The analysis here builds upon our current understanding of vaginal gel deployment and drug delivery, incorporating key features of the gel's environment, fluid production and subsequent gel dilution, and vaginal wall elasticity. We consider the microbicide drug tenofovir as it is the most completely studied drug, in both in vitroand in vivostudies, for use in vaginal gel application. Our goal is to contribute to improved pharmacological understanding of gel functionality, providing a computational tool that can be used in future vaginal microbicide gel design.

Water-Rich Fluid Material Containing Orderly Condensed Proteins.

PubMed

Nojima, Tatsuya; Iyoda, Tomokazu

2017-01-24

A fluid material with high protein content (120-310 mg mL -1 ) was formed through the ordered self-assembly of native proteins segregated from water. This material is instantly prepared by the simple mixing of a protein solution with anionic and cationic surfactants. By changing the ratio of the surfactants based on the electrostatic characteristics of the target protein, we observed that the surfactants could function as a versatile molecular glue for protein assembly. Moreover, these protein assemblies could be disassembled back into an aqueous solution depending on the salt conditions. Owing to the water-retaining properties of the hydrophilic part of surfactants, the proteins in this material are in a water-rich environment, which maintains their native structure and function. The inclusion of water also provides functional extensibility to this material, as demonstrated by the preparation of an enzymatically active gel. We anticipate that the unique features of this material will permit the use of proteins not only in solution but also as elements of integrated functionalized materials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring.

PubMed

He, Yong-Zhi; Fan, Ke-Qiang; Jia, Cui-Juan; Wang, Zhi-Jun; Pan, Wu-Bin; Huang, Li; Yang, Ke-Qian; Dong, Zhi-Yang

2007-05-01

A new gene encoding a thermostable Fe-superoxide dismutase (tcSOD) was identified from a metagenomic library prepared from a hot spring sample. The open reading frame of tcSOD encoded a 211 amino acid protein. The recombinant protein was overexpressed in Escherichia coli and confirmed to be a Fe-SOD with a specific activity of 1,890 U/mg using the pyrogallol method. The enzyme was highly stable at 80 degrees C and retained 50% activity after heat treatment at 95 degrees C for 2 h. It showed striking stability across a wide pH span from 4 to 11. The native form of the enzyme was determined as a homotetramer by analytical ultracentrifugation and gradient native polyacrylamide gel electrophoresis. Fe(2+) was found to be important to SOD activity and to the stability of tcSOD dimer. Comparative modeling analyses of tcSOD tetramer indicate that its high thermostability is mainly due to the presence of a large number of intersubunit ion pairs and hydrogen bonds and to a decrease in solvent accessible hydrophobic surfaces.

Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme

DOE PAGES

Lee, Hui-Ting; Kilburn, D.; Behrouzi, R.; ...

2014-12-05

The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg2+ concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg2+more » concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.« less

Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme

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

Lee, Hui-Ting; Kilburn, D.; Behrouzi, R.

The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg2+ concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg2+more » concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.« less

Purification and characterization of an N alpha-acetyltransferase from Saccharomyces cerevisiae.

PubMed

Lee, F J; Lin, L W; Smith, J A

1988-10-15

N alpha-Acetyltransferase, which catalyzes the transfer of an acetyl group from acetyl coenzyme A to the alpha-NH2 group of proteins and peptides, was isolated from Saccharomyces cerevisiae and demonstrated by protein sequence analysis to be NH2-terminally blocked. The enzyme was purified 4,600-fold to apparent homogeneity by successive purification steps using DEAE-Sepharose, hydroxylapatite, DE52 cellulose, and Affi-Gel blue. The Mr of the native enzyme was estimated to be 180,000 +/- 10,000 by gel filtration chromatography, and the Mr of each subunit was estimated to be 95,000 +/- 2,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme has a pH optimum near 9.0, and its pI is 4.3 as determined by chromatofocusing on Mono-P. The enzyme catalyzed the transfer of an acetyl group to various synthetic peptides, including human adrenocorticotropic hormone (ACTH) (1-24) and its [Phe2] analogue, yeast alcohol dehydrogenase I (1-24), yeast alcohol dehydrogenase II (1-24), and human superoxide dismutase (1-24). These peptides contain either Ser or Ala as NH2-terminal residues which together with Met are the most commonly acetylated NH2-terminal residues (Persson, B., Flinta, C., von Heijne, G., and Jornvall, H. (1985) Eur. J. Biochem. 152, 523-527). Yeast enolase, containing a free NH2-terminal Ala residue, is known not to be N alpha-acetylated in vivo (Chin, C. C. Q., Brewer, J. M., and Wold, F. (1981) J. Biol. Chem. 256, 1377-1384), and enolase (1-24), a synthetic peptide mimicking the protein's NH2 terminus, was not acetylated in vitro by yeast acetyltransferase. The enzyme did not catalyze the N alpha-acetylation of other synthetic peptides including ACTH(11-24), ACTH(7-38), ACTH(18-39), human beta-endorphin, yeast superoxide dismutase (1-24). Each of these peptides has an NH2-terminal residue which is rarely acetylated in proteins (Lys, Phe, Arg, Tyr, Val, respectively). Among a series of divalent cations, Cu2+ and Zn2+ were demonstrated to be the most potent inhibitors. The enzyme was inactivated by chemical modification with diethyl pyrocarbonate and N-bromosuccinimide.

Disintegration kinetics of food gels during gastric digestion and its role on gastric emptying: an in vitro analysis.

PubMed

Guo, Qing; Ye, Aiqian; Lad, Mita; Ferrua, Maria; Dalgleish, Douglas; Singh, Harjinder

2015-03-01

The understanding of the disintegration and gastric emptying of foods in the stomach is important for designing functional foods. In this study, a dynamic stomach model (human gastric simulator, HGS) was employed to investigate the disintegration and subsequent emptying of two differently structured whey protein emulsion gels (soft and hard gels).The gels were mechanically ground into fragments to reproduce the particle size distribution of an in vivo gel bolus. The simulated gel bolus was prepared by mixing gel fragments and artificial saliva, and exposed to 5 hours of simulated gastric digestion in the presence and absence of pepsin. Results showed that regardless of pepsin, the soft gel always disintegrated faster than the hard gel. The presence of pepsin significantly accelerated the disintegration of both gels. In particular, it enhanced abrasion of the soft gel into fine particles (<0.425 mm) after 180 min of processing. The emptying of the gels was influenced by the combined effects of the original particle size of the gel boluses and their disintegration kinetics in the HGS. In the presence or absence of pepsin, the larger particles of the soft gel emptied slower than the hard one during the first 120 min of process. However, in the presence of pepsin, the soft gel emptied faster than the hard one after 120 min because of a higher level of disintegration. These findings highlight the role of food structure, bolus properties and biochemical effects on the disintegration and gastric emptying patterns of gels during gastric digestion.

Internal structure analysis of particle-double network gels used in a gel organ replica

NASA Astrophysics Data System (ADS)

Abe, Mei; Arai, Masanori; Saito, Azusa; Sakai, Kazuyuki; Kawakami, Masaru; Furukawa, Hidemitsu

2016-04-01

In recent years, the fabrication of patient organ replicas using 3D printers has been attracting a great deal of attention in medical fields. However, the cost of these organ replicas is very high as it is necessary to employ very expensive 3D printers and printing materials. Here we present a new gel organ replica, of human kidney, fabricated with a conventional molding technique, using a particle-double network hydrogel (P-DN gel). The replica is transparent and has the feel of a real kidney. It is expected that gel organ replicas produced this way will be a useful tool for the education of trainee surgeons and clinical ultrasonography technologists. In addition to developing a gel organ replica, the internal structure of the P-DN gel used is also discussed. Because the P-DN gel has a complex structure comprised of two different types of network, it has not been possible to investigate them internally in detail. Gels have an inhomogeneous network structure. If it is able to get a more uniform structure, it is considered that this would lead to higher strength in the gel. In the present study we investigate the structure of P-DN gel, using the gel organ replica. We investigated the internal structure of P-DN gel using Scanning Microscopic Light Scattering (SMILS), a non-contacting and non-destructive.

Maleimidobenzoyl-G-actin: Structural properties and interaction with skeletal myosin subfragment-1

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

Bettache, N.; Bertrand, R.; Kassab, R.

1990-09-25

The authors have investigated various structural and interaction properties of maleimidobenzoyl-G-actin (MBS-actin), a new, internally cross-linked G-actin derivative that does not exhibit, at moderate protein concentration, the salt-and myosin subfragment 1 (S-1)--induced polymerizations of G-actin and reacts reversibly and covalently in solution with S-1 at or near the F-actin binding region of the heavy chain. The far-ultraviolet CD spectrum and {alpha}-helix content of the MBS-actin were identical with those displayed by native G-actin. {sup 45}Ca{sup 2+} measurements showed the same content of tightly bound Ca{sup 2+} in MBS-actin as in G-actin and the EDTA treatment of the modified protein promotedmore » the same red shift of the intrinsic fluorescence spectrum as observed with native G-actin. Incubation of concentrated MBS-actin solutions with 100 mM KCl+5 mM MgCl{sub 2} led to the polymerization of the actin derivative when the critical monomer concentration reached 1.6mg/mL, at 25{degree}C, pH 8.0. The MBS-F-actin formed activated the Mg{sup 2+}-ATPase of S-1 to the same extent as native F-actin. The MBS-G-actin exhibited a DNase I inhibitor activity very close to that found with native G-actin and was to be at all affected by its specific covalent conjugation to S-1. This finding led them to isolate, for the first time, by gel filtration, a ternary complex comprising DNase I tightly bound to MBS-actin cross-linked to the S-1 heavy chain, demonstrating that S-1 and DNase I bind at distinct sites on G-actin. Collectively, the data illustrate further the nativeness of the MBS-G-actin and its potential use in solution studies of the actin-myosin head interactions.« less

The endogenous fluorescence of fibroblast in collagen gels as indicator of stiffness of the extracellular matrix

NASA Astrophysics Data System (ADS)

Padilla-Martinez, J. P.; Ortega-Martinez, A.; Franco, W.

2016-03-01

The stiffness or rigidity of the extracellular matrix (ECM) regulates cell response. Established mechanical tests to measure stiffness, such as indentation and tensile tests, are invasive and destructive to the sample. Endogenous or native molecules to cells and ECM components, like tryptophan and cross-links of collagen, display fluorescence upon irradiation with ultraviolet light. Most likely, the concentration of these endogenous fluorophores changes as the stiffness of the ECM changes. In this work we investigate the endogenous fluorescence of collagen gels containing fibroblasts as a non-invasive non-destructive method to measure stiffness of the ECM. Human fibroblast cells were cultured in three-dimensional gels of type I collagen (50,000 cells/ml). This construct is a simple model of tissue contraction. During contraction, changes in the excitation-emission matrix (a fluorescence map in the 240-520/290-530 nm range) of constructs were measured with a spectrofluoremeter, and changes in stiffness were measured with a standard indentation test over 16 days. Results show that a progressive increase in fluorescence of the 290/340 nm excitation-emission pair correlates with a progressive increase in stiffness (r=0.9, α=0.5). The fluorescence of this excitation-emission pair is ascribed to tryptophan and variations in the fluorescence of this pair correlate with cellular proliferation. In this tissue model, the endogenous functional fluorescence of proliferating fibroblast cells is a biomechanical marker of stiffness of the ECM.

Effective production of resistant starch using pullulanase immobilized onto magnetic chitosan/Fe3O4 nanoparticles.

PubMed

Long, Jie; Zhang, Bao; Li, Xingfei; Zhan, Xiaobei; Xu, Xueming; Xie, Zhengjun; Jin, Zhengyu

2018-01-15

In this study, pullulanase was firstly immobilized by covalent bonding onto chitosan/Fe 3 O 4 nanoparticles or encapsulation in sol-gel after bonding onto chitosan/Fe 3 O 4 nanoparticles, and then the immobilized pullulanase was used for the effective production of resistant starch (RS). The highest RS content (35.1%) was obtained under the optimized condition of pH 4.4, enzyme concentration of 10ASPU/g and hydrolysis time of 12h when debranched by free pullulsanase, indicating that RS content was significantly (p<0.05) increased when compared to native starch (4.3%) and autoclaved starch (12.5%). Under these conditions, the immobilized pullulanase (10ASPU/g dry starch) yielded higher RS content compared to free enzyme (10ASPU/g dry starch), especially, the pullulanse immobilized by sol-gel encapsulation yielded the highest RS content (43.4%). Moreover, compared to starches hydrolyzed by free pullulanase, starches hydrolyzed by immobilized pullulanase showed a different saccharide profile of starch hydrolysate, including a stronger peak C (MW=5.0×10 3 ), as well as exhibited an additional absorption peak around 140°C. Reusability results demonstrated that pullulanase immobilized by sol-gel encapsulation had the advantages of producing higher RS content as well as better operational stability compared to pullulanase immobilized by cross-linking. The resulting enhanced RS content generated by the process described in this work could be used as an adjunct in food processing industries. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid, quantitative analysis of ppm/ppb nicotine using surface-enhanced Raman scattering from polymer-encapsulated Ag nanoparticles (gel-colls).

PubMed

Bell, Steven E J; Sirimuthu, Narayana M S

2004-11-01

Rapid, quantitative SERS analysis of nicotine at ppm/ppb levels has been carried out using stable and inexpensive polymer-encapsulated Ag nanoparticles (gel-colls). The strongest nicotine band (1030 cm(-1)) was measured against d(5)-pyridine internal standard (974 cm(-1)) which was introduced during preparation of the stock gel-colls. Calibration plots of I(nic)/I(pyr) against the concentration of nicotine were non-linear but plotting I(nic)/I(pyr) against [nicotine](x)(x = 0.6-0.75, depending on the exact experimental conditions) gave linear calibrations over the range (0.1-10 ppm) with R(2) typically ca. 0.998. The RMS prediction error was found to be 0.10 ppm when the gel-colls were used for quantitative determination of unknown nicotine samples in 1-5 ppm level. The main advantages of the method are that the gel-colls constitute a highly stable and reproducible SERS medium that allows high throughput (50 sample h(-1)) measurements.

A Sol-gel Integrated Dual-readout Microarray Platform for Quantification and Identification of Prostate-specific Antigen.

PubMed

Lee, SangWook; Lee, Jong Hyun; Kwon, Hyuck Gi; Laurell, Thomas; Jeong, Ok Chan; Kim, Soyoun

2018-01-01

Here, we report a sol-gel integrated affinity microarray for on-chip matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) that enables capture and identification of prostate?specific antigen (PSA) in samples. An anti-PSA antibody (H117) was mixed with a sol?gel, and the mixture was spotted onto a porous silicon (pSi) surface without additional surface modifications. The antibody easily penetrates the sol-gel macropore fluidic network structure, making possible high affinities. To assess the capture affinity of the platform, we performed a direct assay using fluorescein isothiocyanate-labeled PSA. Pure PSA was subjected to on-chip MALDI-TOF-MS analysis, yielding three clear mass peptide peaks (m/z = 1272, 1407, and 1872). The sol-gel microarray platform enables dual readout of PSA both fluorometric and MALDI-TOF MS analysis in biological samples. Here we report a useful method for a means for discovery of biomarkers in complex body fluids.

Performance of a commercial optical CT scanner and polymer gel dosimeters for 3-D dose verification

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

Xu, Y.; Wuu, C.-S.; Maryanski, Marek J.

2004-11-01

Performance analysis of a commercial three-dimensional (3-D) dose mapping system based on optical CT scanning of polymer gels is presented. The system consists of BANG{sup reg}3 polymer gels (MGS Research, Inc., Madison, CT), OCTOPUS{sup TM} laser CT scanner (MGS Research, Inc., Madison, CT), and an in-house developed software for optical CT image reconstruction and 3-D dose distribution comparison between the gel, film measurements and the radiation therapy treatment plans. Various sources of image noise (digitization, electronic, optical, and mechanical) generated by the scanner as well as optical uniformity of the polymer gel are analyzed. The performance of the scanner ismore » further evaluated in terms of the reproducibility of the data acquisition process, the uncertainties at different levels of reconstructed optical density per unit length and the effects of scanning parameters. It is demonstrated that for BANG{sup registered}3 gel phantoms held in cylindrical plastic containers, the relative dose distribution can be reproduced by the scanner with an overall uncertainty of about 3% within approximately 75% of the radius of the container. In regions located closer to the container wall, however, the scanner generates erroneous optical density values that arise from the reflection and refraction of the laser rays at the interface between the gel and the container. The analysis of the accuracy of the polymer gel dosimeter is exemplified by the comparison of the gel/OCT-derived dose distributions with those from film measurements and a commercial treatment planning system (Cadplan, Varian Corporation, Palo Alto, CA) for a 6 cmx6 cm single field of 6 MV x rays and a 3-D conformal radiotherapy (3DCRT) plan. The gel measurements agree with the treatment plans and the film measurements within the '3%-or-2 mm' criterion throughout the usable, artifact-free central region of the gel volume. Discrepancies among the three data sets are analyzed.« less

Effect of pullulan on the water distribution, microstructure and textural properties of rice starch gels during cold storage.

PubMed

Chen, Long; Tian, Yaoqi; Tong, Qunyi; Zhang, Zipei; Jin, Zhengyu

2017-01-01

The effects of pullulan on the water distribution, microstructure and textural properties of rice starch gels during cold storage were investigated by low field-nuclear magnetic resonance (LF-NMR), scanning electron microscope (SEM), and texture profile analysis (TPA). The addition of pullulan reduced the transversal relaxation time of rice starch gels during cold storage. The microstructure of rice starch gel with 0.5% pullulan was denser and more uniform compared with that of rice starch without pullulan in each period of storage time. With regard to textural properties, 0.01% pullulan addition did not significantly change the texture of rice starch gels, while 0.5% pullulan addition appeared to reduce the hardness and retain the springiness of rice starch gels (P⩽0.05). The restriction effects of pullulan on water mobility and starch retrogradation were hypothesized to be mainly responsible for the water retention, gel structure maintenance, and modification of the textural attributes of rice starch gels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cold therapy for the management of pain associated with deep breathing and coughing post-cardiac surgery.

PubMed

Chailler, Myrianne; Ellis, Jacqueline; Stolarik, Anne; Woodend, Kirsten

2010-01-01

Coughing has been identified as the most painful experience post cardiac surgery. Participants (n = 32), in a randomized crossover trial, applied a frozen gel pack to their sternal incision dressing before performing deep breathing and coughing (DB & C) exercises. Pain scores from 0 to 10 at rest were compared with pain scores post DB & C with and without the gel pack. Participants were also asked to describe their sensations with the frozen gel pack, as well as their preferences for gel pack application. The repeated measures analysis of variance revealed a significant reduction in pain scores between pre- and post-application of the gel pack (F = 28.69, p < .001). There were 22 (69%) participants who preferred the application of the gel pack compared with no gel pack. All 32 (100%) participants would reapply the gel pack in the future. This study demonstrates that cold therapy can be used to manage sternal incisional pain when DB & C.

Analysis of the adhesion of Pseudomonas putida NCIB 9816-4 to a silica gel as a model soil using extended DLVO theory.

PubMed

Hwang, Geelsu; Lee, Chang-Ha; Ahn, Ik-Sung; Mhin, Byung Jin

2010-07-15

The extended Derjaguin-Landau-Verwey-Overbeek (DLVO) theory was applied to explain the hydrophobic interaction-mediated adhesion of Pseudomonas putida NCIB 9816-4 to soil. Soil particles are heterogeneous, and it is difficult to define consistent physico-chemical properties such as a contact angle and zeta potential. Hence, a silica gel and a silanized (3-aminopropyltriethoxysilane-coated) silica gel, which showed greater hydrophobicity than the unmodified silica gel, were used as model soils. Gibbs energies for the cell adhesion to the silica gels were calculated with the physico-chemical properties of the microbes and the silica gels and then plotted as a function of the separation distance. The extended DLVO theory successfully explained that the adhesion of P. putida NCIB 9816-4 to the silica gel, a model soil, was primarily caused by hydrophobic interaction. 2010 Elsevier B.V. All rights reserved.

Development of poloxamer gel formulations via hot-melt extrusion technology.

PubMed

Mendonsa, Nicole S; Murthy, S Narasimha; Hashemnejad, Seyed Meysam; Kundu, Santanu; Zhang, Feng; Repka, Michael A

2018-02-15

Poloxamer gels are conventionally prepared by the "hot" or the "cold" process. But these techniques have some disadvantages such as high energy consumption, requires expensive equipment and often have scale up issues. Therefore, the objective of this work was to develop poloxamer gels by hot-melt extrusion technology. The model drug selected was ketoprofen. The formulations developed were 30% and 40% poloxamer gels. Of these formulations, the 30% poloxamer gels were selected as ideal gels. DSC and XRD studies showed an amorphous nature of the drug after extrusion. It was observed from the permeation studies that with increasing poloxamer concentration, a decrease in drug permeation was obtained. Other studies conducted for the formulations included in-vitro release studies, texture analysis, rheological studies and pH measurements. In conclusion, the hot-melt extrusion technology could be successfully employed to develop poloxamer gels by overcoming the drawbacks associated with the conventional techniques. Published by Elsevier B.V.

Automated apparatus for producing gradient gels

DOEpatents

Anderson, N.L.

1983-11-10

Apparatus for producing a gradient gel which serves as a standard medium for a two-dimensional analysis of proteins, the gel having a density gradient along its height formed by a variation in gel composition, with the apparatus including first and second pumping means each including a plurality of pumps on a common shaft and driven by a stepping motor capable of providing small incremental changes in pump outputs for the gel ingredients, the motors being controlled, by digital signals from a digital computer, a hollow form or cassette for receiving the gel composition, means for transferring the gel composition including a filler tube extending near the bottom of the cassette, adjustable horizontal and vertical arms for automatically removing and relocating the filler tube in the next cassette, and a digital computer programmed to automatically control the stepping motors, arm movements, and associated sensing operations involving the filling operation.

Automated apparatus for producing gradient gels

DOEpatents

Anderson, Norman L.

1986-01-01

Apparatus for producing a gradient gel which serves as a standard medium for a two-dimensional analysis of proteins, the gel having a density gradient along its height formed by a variation in gel composition, with the apparatus including first and second pumping means each including a plurality of pumps on a common shaft and driven by a stepping motor capable of providing small incremental changes in pump outputs for the gel ingredients, the motors being controlled, by digital signals from a digital computer, a hollow form or cassette for receiving the gel composition, means for transferring the gel composition including a filler tube extending near the bottom of the cassette, adjustable horizontal and vertical arms for automatically removing and relocating the filler tube in the next cassette, and a digital computer programmed to automatically control the stepping motors, arm movements, and associated sensing operations involving the filling operation.

Infrared and Raman spectra of triacetoxyvinylsilane, aqueous sol-gel and xerogel

NASA Astrophysics Data System (ADS)

Li, Ying-Sing; Ba, Abdul; Mahmood, Maleeha S.

2009-04-01

Triacetoxyvinylsilane (TAVS) has been used as a precursor to prepare sol-gel under aqueous conditions. The sol-gel product has been applied for the surface treatment of aluminum. Infrared and Raman spectra have been collected for TAVS and for TAVS sol-gel, xerogel and sol-gel-coated aluminum. Vibrational analyses have been suggested for the recorded spectra based essentially on the group frequencies and the spectral variation with the change of the sol-gel product states and the vibrational assignments of similar molecules. From the recorded infrared and Raman spectra of the sol-gel and xerogel, it is found that the sol-gel produced in the process with TAVS is essentially the same as that prepared from vinyltriethoxysilane. Thermo-gravimetric analysis (TGA) of TAVS xerogel has been conducted, and an explanation has been given in coordination with the results obtained from IR spectroscopic study of the xerogels cured at different temperatures. The study has demonstrated the thermal effect on the condensation of the sol-gel process and on the vinyl decomposition of TAVS xerogel.

Purification and partial characterization of a new mannose/glucose-specific lectin from Dialium guineense Willd seeds that exhibits toxic effect.

PubMed

Bari, Alfa U; Silva, Helton C; Silva, Mayara T L; Pereira Júnior, Francisco N; Cajazeiras, João B; Sampaio, Alexandre H; Leal, Rodrigo B; Teixeira, Edson H; Rocha, Bruno A M; Nascimento, Kyria S; Nagano, Celso S; Cavada, Benildo S

2013-08-01

A new mannose/glucose-specific lectin, named DigL, was purified from seeds of Dialium guineense by a single step using a Sepharose 4b-Mannose affinity chromatography column. DigL strongly agglutinated rabbit erythrocytes and was inhibited by d-mannose, d-glucose, and derived sugars, especially α-methyl-d-mannopyranoside and N-acetyl-d-glucosamine. DigL has been shown to be a stable protein, maintaining its hemagglutinating activity after incubation at a wide range of temperature and pH values and after incubation with EDTA. DigL is a glycoprotein composite by approximately 2.9% of carbohydrates by weight. By sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis, the purified DigL exhibited an electrophoretic profile consisting of a broad band of 28-30 kDa. Analysis using electrospray ionization mass spectrometry indicated that purified DigL possesses a molecular average mass of 28 452 ± 2 Da and shows the presence of possible glycoforms. In addition, DigL exhibited an intermediary toxic effect on Artemia sp. nauplii, and this effect was both dependent on native structure and mediated by a carbohydrate-binding site. Copyright © 2013 John Wiley & Sons, Ltd.

Reanalysis and semantic persistence in native and non-native garden-path recovery.

PubMed

Jacob, Gunnar; Felser, Claudia

2016-01-01

We report the results from an eye-movement monitoring study investigating how native and non-native speakers of English process temporarily ambiguous sentences such as While the gentleman was eating the burgers were still being reheated in the microwave, in which an initially plausible direct-object analysis is first ruled out by a syntactic disambiguation (were) and also later on by semantic information (being reheated). Both participant groups showed garden-path effects at the syntactic disambiguation, with native speakers showing significantly stronger effects of ambiguity than non-native speakers in later eye-movement measures but equally strong effects in first-pass reading times. Ambiguity effects at the semantic disambiguation and in participants' end-of-trial responses revealed that for both participant groups, the incorrect direct-object analysis was frequently maintained beyond the syntactic disambiguation. The non-native group showed weaker reanalysis effects at the syntactic disambiguation and was more likely to misinterpret the experimental sentences than the native group. Our results suggest that native language (L1) and non-native language (L2) parsing are similar with regard to sensitivity to syntactic and semantic error signals, but different with regard to processes of reanalysis.

The expression of native and cultured human retinal pigment epithelial cells grown in different culture conditions.

PubMed

Tian, J; Ishibashi, K; Honda, S; Boylan, S A; Hjelmeland, L M; Handa, J T

2005-11-01

To determine the transcriptional proximity of retinal pigment epithelium (RPE) cells grown under different culture conditions and native RPE. ARPE-19 cells were grown under five conditions in 10% CO(2): "subconfluent" in DMEM/F12+10% FBS, "confluent" in serum and serum withdrawn, and "differentiated" for 2.5 months in serum and serum withdrawn medium. Native RPE was laser microdissected. Total RNA was extracted, reverse transcribed, and radiolabelled probes were hybridised to an array containing 5,353 genes. Arrays were evaluated by hierarchical cluster analysis and significance analysis of microarrays. 78% of genes were expressed by native RPE while 45.3--47.7% were expressed by ARPE-19 cells, depending on culture condition. While the most abundant genes were expressed by native and cultured cells, significant differences in low abundance genes were seen. Hierarchical cluster analysis showed that confluent and differentiated, serum withdrawn cultures clustered closest to native RPE, and that serum segregated cultured cells from native RPE. The number of differentially expressed genes and their function, and profile of expressed and unexpressed genes, demonstrate differences between native and cultured cells. While ARPE-19 cells have significant value for studying RPE behaviour, investigators must be aware of how culture conditions can influence the mRNA phenotype of the cell.

Analysis of charge transport in gels containing polyoxometallates using methods of different sensitivity to migration.

PubMed

Caban, Karolina; Lewera, Adam; Zukowska, Grazyna Z; Kulesza, Pawel J; Stojek, Zbigniew; Jeffrey, Kenneth R

2006-08-04

Two methods have been used for examination of transport of charge in gels soaked with DMF and containing dissolved polyoxometallates. The first method is based on the analysis of both Cottrellian and steady-state currents and therefore is capable of giving the concentration of the electroactive redox centres and their transport (diffusion-type) coefficient. The second method provides the real diffusion coefficients, i.e. transport coefficients free of migrational influence, for both the substrate and the product of the electrode reaction. Several gels based on poly(methyl methacrylate), with charged (addition of 1-acrylamido-2-methyl-2-propanesulphonic acid to the polymerization mixture) and uncharged chains, have been used in the investigation. The ratio obtained for the diffusion coefficient (second method) and transport coefficient (first method) was smaller for the gels containing charged polymer chains than for the gels with uncharged chains. In part these changes could be explained by the contribution of migration to the transport of polyoxomatallates in the gels. However, the impact of the changes in the polymer-channel capacity at the electrode surface while the electrode process proceeds was also considered. These structural changes should affect differently the methods based on different time domains.

Preparation and characterization of sustained-release rotigotine film-forming gel.

PubMed

Li, Xiang; Zhang, Renyu; Liang, Rongcai; Liu, Wei; Wang, Chenhui; Su, Zhengxing; Sun, Fengying; Li, Youxin

2014-01-02

The aim of this study was to develop a film-forming gel formulation of rotigotine with hydroxypropyl cellulose (HPC) and Carbomer 934. To optimize this formulation, we applied the Response Surface Analysis technique and evaluated the gel's pharmacokinetic properties. The factors chosen for factorial design were the concentration of rotigotine, the proportion of HPC and Carbomer 934, and the concentration of ST-Elastomer 10. Each factor was varied over three levels: low, medium and high. The gel formulation was evaluated and optimized according to its accumulated permeation rate (Flux) through Franz-type diffusion. A pharmacokinetic study of rotigotine gel was performed with rabbits. The Flux of the optimized formulation reached the maximum (199.17 μg/cm(2)), which was 3% rotigotine and 7% ST-Elastomer 10 with optimal composition of HPC: Carbomer 934 (5:1). The bioavailability of the optimized formulation compared with intravenous administration was approximately 20%. A film-forming gel of rotigotine was successfully developed using the response surface analysis technique. The results of this study may be helpful in finding an optimum formulation for transdermal delivery of a drug. The product may improve patients' compliance and provide better efficacy. Copyright © 2013 Elsevier B.V. All rights reserved.

The influence of polymer molecular weight in lamellar gels based on PEG-lipids.

PubMed Central

Warriner, H E; Keller, S L; Idziak, S H; Slack, N L; Davidson, P; Zasadzinski, J A; Safinya, C R

1998-01-01

We report x-ray scattering, rheological, and freeze-fracture and polarizing microscopy studies of a liquid crystalline hydrogel called Lalpha,g. The hydrogel, found in DMPC, pentanol, water, and PEG-DMPE mixtures, differs from traditional hydrogels, which require high MW polymer, are disordered, and gel only at polymer concentrations exceeding an "overlap" concentration. In contrast, the Lalpha,g uses very low-molecular-weight polymer-lipids (1212, 2689, and 5817 g/mole), shows lamellar order, and requires a lower PEG-DMPE concentration to gel as water concentration increases. Significantly, the Lalpha,g contains fluid membranes, unlike Lbeta' gels, which gel via chain ordering. A recent model of gelation in Lalpha phases predicts that polymer-lipids both promote and stabilize defects; these defects, resisting shear in all directions, then produce elasticity. We compare our observations to this model, with particular attention to the dependence of gelation on the PEG MW used. We also use x-ray lineshape analysis of scattering from samples spanning the fluid-gel transition to obtain the elasticity coefficients kappa and B; this analysis demonstrates that although B in particular depends strongly on PEG-DMPE concentration, gelation is uncorrelated to changes in membrane elasticity. PMID:9649387

A preliminary study on the use of FX-Glycine gel and an in-house optical cone beam CT readout for IMRT and RapidArc verification

NASA Astrophysics Data System (ADS)

Ravindran, Paul B.; Ebenezer, Suman Babu S.; Winfred, Michael Raj; Amalan, S.

2017-05-01

The radiochromic FX gel with Optical CT readout has been investigated by several authors and has shown promising results for 3D dosimetry. One of the applications of the gel dosimeters is their use in 3D dose verification for IMRT and RapidArc quality assurance. Though polymer gel has been used successfully for clinical dose verification, the use of FX gel for clinical dose verification with optical cone beam CT needs further validation. In this work, we have used FX gel and an in- house optical readout system for gamma analysis between the dose matrices of measured dose distribution and a treatment planning system (TPS) calculated dose distribution for a few test cases.

Functional expression of a Bombyx mori cocoonase: potential application for silk degumming.

PubMed

Rodbumrer, Prangprapai; Arthan, Dumrongkiet; Uyen, Utai; Yuvaniyama, Jirundon; Svasti, Jisnuson; Wongsaengchantra, Pramvadee Y

2012-12-01

Cocoon, a shelter for larva development to silk moth, contains the fibrous protein fibroin, which is coated by the globular protein sericin. Emergence of the silk moth requires the action of cocoonase, a protease secreted by the pupa. The full-length prococoonase cDNA, with 780 bp open reading frame encoding 260 amino acids, was cloned by reverse transcription from total RNA of the head of 6-day-old Thai-silk Bombyx mori pupa. Only the gene fragment lacking the propeptide encoding sequence was successfully expressed in Pichia pastoris, yielding an extracellularly active cocoonase. The recombinant cocoonase was purified to homogeneity by 80% ammonium-sulfate fractionation and CM-Sepharose chromatography, and its internal peptide sequences were analyzed by nano liquid chromatography-mass spectrometry/mass spectrometry. This monomeric protein has native molecular weight of 26 kDa by gel exclusion analysis and 25 kDa subunit size by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The enzyme hydrolyses sericin but does not hydrolyse fibroin, as shown by radial diffusion on thin-layer enzyme assay (RD-TEA). Scanning electron microscopy showed that purified recombinant cocoonase could remove sericin from natural silk completely in 24 h, without damaging fibroin, using only 1 immobilized sericin unit (ISU) of enzyme as determined by RD-TEA. Natural cocoonase isolated from B. mori pupa could also digest sericin effectively, but required more enzymes (2 ISU) and longer time (48 h). In comparison, a commercial enzyme, alcalase, with the same activity not only showed less complete digestion of sericin but also caused damage of fibroin. These results suggest that recombinant B. mori cocoonase is potentially useful for silk degumming.

Purification and partial characterization of an aminopeptidase from the midgut tissue of Dysdercus peruvianus.

PubMed

Costa, Inês A; Samuels, Richard I; Bifano, Thaís D; Terra, Walter R; Silva, Carlos P

2011-03-01

The surface of midgut cells in Hemiptera is ensheathed by a lipoprotein membrane (the perimicrovillar membrane), which delimits a closed compartment with the microvillar membrane, the so-called perimicrovillar space. In Dysdercus peruvianus midgut perimicrovillar space a soluble aminopeptidase maybe involved in the digestion of oligopeptides and proteins ingested in the diet. This D. peruvianus aminopeptidase was purified to homogeneity by ion-exchange chromatography on an Econo-Q column, hydrophobic interaction chromatography on phenyl-agarose column and preparative polyacrylamide gel electrophoresis. The results suggested that there is a single molecular species of aminopeptidase in D. peruvianus midgut. Molecular mass values for the aminopeptidase were estimated to be 106kDa (gel filtration) and 55kDa (SDS-PAGE), suggesting that the enzyme occurs as a dimer under native conditions. Kinetic data showed that D. peruvianus aminopeptidase hydrolyzes the synthetic substrates LpNA, RpNA, AβNA and AsnMCA (K(m)s 0.65, 0.14, 0.68 and 0.74mM, respectively). The aminopeptidase activity upon LpNA was inhibited by EDTA and 1,10-phenanthroline, indicating the importance of metal ions in enzyme catalysis. One partial sequence of BLAST-identified aminopeptidase was found by random sequencing of the D. peruvianus midgut cDNA library. Semi-quantitative RT-PCR analysis showed that the aminopeptidase genes were expressed throughout the midgut epithelium, in the epithelia of V1, V2 and V3, Malphigian tubules and fat body, but it was not expressed in the salivary glands. These results are important in furthering our understanding of the digestive process in this pest species. Copyright © 2010 Elsevier Inc. All rights reserved.

Spontaneous mutation reveals influence of exopolysaccharide on Lactobacillus johnsonii surface characteristics.

PubMed

Horn, Nikki; Wegmann, Udo; Dertli, Enes; Mulholland, Francis; Collins, Samuel R A; Waldron, Keith W; Bongaerts, Roy J; Mayer, Melinda J; Narbad, Arjan

2013-01-01

As a competitive exclusion agent, Lactobacillus johnsonii FI9785 has been shown to prevent the colonization of selected pathogenic bacteria from the chicken gastrointestinal tract. During growth of the bacterium a rare but consistent emergence of an altered phenotype was noted, generating smooth colonies in contrast to the wild type rough form. A smooth colony variant was isolated and two-dimensional gel analysis of both strains revealed a protein spot with different migration properties in the two phenotypes. The spot in both gels was identified as a putative tyrosine kinase (EpsC), associated with a predicted exopolysaccharide gene cluster. Sequencing of the epsC gene from the smooth mutant revealed a single substitution (G to A) in the coding strand, resulting in the amino acid change D88N in the corresponding gene product. A native plasmid of L. johnsonii was engineered to produce a novel vector for constitutive expression and this was used to demonstrate that expression of the wild type epsC gene in the smooth mutant produced a reversion to the rough colony phenotype. Both the mutant and epsC complemented strains had increased levels of exopolysaccharides compared to the wild type strain, indicating that the rough phenotype is not solely associated with the quantity of exopolysaccharide. Another gene in the cluster, epsE, that encoded a putative undecaprenyl-phosphate galactosephosphotransferase, was deleted in order to investigate its role in exopolysaccharide biosynthesis. The ΔepsE strain exhibited a large increase in cell aggregation and a reduction in exopolysaccharide content, while plasmid complementation of epsE restored the wild type phenotype. Flow cytometry showed that the wild type and derivative strains exhibited clear differences in their adhesive ability to HT29 monolayers in tissue culture, demonstrating an impact of EPS on surface properties and bacteria-host interactions.

Temperature dependent characteristics of a recombinant infectious hematopoietic necrosis virus glycoprotein produced in insect cells.

PubMed

Cain, K D; Byrne, K M; Brassfield, A L; LaPatra, S E; Ristow, S S

1999-04-15

A recombinant infectious hematopoietic necrosis virus (IHNV) glycoprotein (G protein) was produced in insect cells using a baculovirus vector (Autographa californica nuclear polyhedrosis virus). Characteristics of this protein were evaluated in relation to native viral G protein. A full-length (1.6 kb) cDNA copy of the glycoprotein gene of IHNV was inserted into the baculovirus vector under control of the polyhedrin promoter. High levels of G protein (approximately 0.5 microgram/1 x 10(5) cells) were produced in Spodoptera frugiperda (Sf9) cells following recombinant baculovirus infection. Analysis of cell lysates by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot revealed a recombinant IHNV G of slightly higher mobility on the gel than the viral G protein. Differences in mobility were abrogated by endoglycosidase treatment. When the recombinant G protein was produced in insect cells at 20 degrees C (RecGlow), immunostaining and cell fusion activity demonstrated surface localization of the protein. In contrast, when recombinant protein was produced at 27 degrees C (RecGhigh), G protein was sequestered within the cell, suggesting that at the 2 different temperatures processing differences may exist. Eleven monoclonal antibodies (MAbs) were tested by immunoblotting for reactivity to the recombinant G protein. All 11 MAbs reacted to the reduced proteins. Four MAbs recognized both RecGhigh and RecGlow under non-reducing conditions; however, 1 neutralizing MAb (92A) recognized RecGlow but failed to react to RecGhigh under non-reducing conditions. This suggests that differences exist between RecGlow and RecGhigh which may have implications in the development of a properly folded recombinant G protein with the ability to elicit protective immunity in fish.

Cloning and Expression of a Phloretin Hydrolase Gene from Eubacterium ramulus and Characterization of the Recombinant Enzyme

PubMed Central

Schoefer, Lilian; Braune, Annett; Blaut, Michael

2004-01-01

Phloretin hydrolase catalyzes the hydrolytic C-C cleavage of phloretin to phloroglucinol and 3-(4-hydroxyphenyl)propionic acid during flavonoid degradation in Eubacterium ramulus. The gene encoding the enzyme was cloned by screening a gene library for hydrolase activity. The insert of a clone conferring phloretin hydrolase activity was sequenced. Sequence analysis revealed an open reading frame of 822 bp (phy), a putative promoter region, and a terminating stem-loop structure. The deduced amino acid sequence of phy showed similarities to a putative protein of the 2,4-diacetylphloroglucinol biosynthetic operon from Pseudomonas fluorescens. The phloretin hydrolase was heterologously expressed in Escherichia coli and purified. The molecular mass of the native enzyme was approximately 55 kDa as determined by gel filtration. The results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the deduced amino acid sequence of phy indicated molecular masses of 30 and 30.8 kDa, respectively, suggesting that the enzyme is a homodimer. The recombinant phloretin hydrolase catalyzed the hydrolysis of phloretin to equimolar amounts of phloroglucinol and 3-(4-hydroxyphenyl)propionic acid. The optimal temperature and pH of the catalyzed reaction mixture were 37°C and 7.0, respectively. The Km for phloretin was 13 ± 3 μM and the kcat was 10 ± 2 s−1. The enzyme did not transform phloretin-2′-glucoside (phloridzin), neohesperidin dihydrochalcone, 1,3-diphenyl-1,3-propandione, or trans-1,3-diphenyl-2,3-epoxy-propan-1-one. The catalytic activity of the phloretin hydrolase was reduced by N-bromosuccinimide, o-phenanthroline, N-ethylmaleimide, and CuCl2 to 3, 20, 35, and 85%, respectively. Phloroglucinol and 3-(4-hydroxyphenyl)propionic acid reduced the activity to 54 and 70%, respectively. PMID:15466559

Three-Dimensional Coculture of Meniscal Cells and Mesenchymal Stem Cells in Collagen Type I Hydrogel on a Small Intestinal Matrix-A Pilot Study Toward Equine Meniscus Tissue Engineering.

PubMed

Kremer, Antje; Ribitsch, Iris; Reboredo, Jenny; Dürr, Julia; Egerbacher, Monika; Jenner, Florien; Walles, Heike

2017-05-01

Meniscal injuries are the most frequently encountered soft tissue injuries in the equine stifle joint. Due to the inherent limited repair potential of meniscal tissue, meniscal injuries do not only affect the meniscus itself but also lead to impaired joint homeostasis and secondary osteoarthritis. The presented study compares 3D coculture constructs of primary equine mesenchymal stem cells (MSC) and meniscus cells (MC) seeded on three different scaffolds-a cell-laden collagen type I hydrogel (Col I gel), a tissue-derived small intestinal matrix scaffold (SIS-muc) and a combination thereof-for their qualification to be applied for meniscus tissue engineering. To investigate cell attachment of primary MC and MSC on SIS-muc matrix SEM pictures were performed. For molecular analysis, lyophilized samples of coculture constructs with different cell ratios (100% MC, 100% MSC, and 50% MC and 50% MSC, 20% MC, and 80% MSC) were digested and analyzed for DNA and GAG content. Active matrix remodeling of 3D coculture models was indicated by matrix metalloproteinases detection. For comparison of tissue-engineered constructs with the histologic architecture of natural equine menisci, paired lateral and medial menisci of 15 horses representing different age groups were examined. A meniscus phenotype with promising similarity to native meniscus tissue in its GAG/DNA expression in addition to Col I, Col II, and Aggrecan production was achieved using a scaffold composed of Col I gel on SIS-muc combined with a coculture of MC and MSC. The results encourage further development of this scaffold-cell combination for meniscus tissue engineering.

Effects of copper ions on the characteristics of egg white gel induced by strong alkali.

PubMed

Shao, Yaoyao; Zhao, Yan; Xu, Mingsheng; Chen, Zhangyi; Wang, Shuzhen; Tu, Yonggang

2017-09-01

This study investigated the effects of copper ions on egg white (EW) gel induced by strong alkali. Changes in gel characteristics were examined through texture profile analysis, scanning electron microscopy (SEM), and chemical methods. The value of gel strength reached its maximum when 0.1% copper ions was added. However, the lowest cohesiveness values were observed at 0.1%. The springiness of gel without copper ions was significantly greater than the gel with copper ions added. SEM results illustrated that the low concentration of copper ions contributes to a dense and uniform gel network, and an open matrix was formed at 0.4%. The free and total sulphhydryl group content in the egg white protein gel significantly decreased with the increased copper. The increase of copper ions left the contents of ionic and hydrogen bonds basically unchanged, hydrophobic interaction presented an increasing trend, and the disulfide bond exhibited a completely opposite change. The change of surface hydrophobicity proved that the main binding force of copper induced gel was hydrophobic interaction. However, copper ions had no effect on the protein component of the gels. Generally, a low level of copper ions facilitates protein-protein association, which is involved in the characteristics of gels. Instead, high ionic strength had a negative effect on gels induced by strong alkali. © 2017 Poultry Science Association Inc.

Hydroponics gel as a new electrolyte gelling agent for alkaline zinc-air cells

NASA Astrophysics Data System (ADS)

Othman, R.; Basirun, W. J.; Yahaya, A. H.; Arof, A. K.

The viability of hydroponics gel as a new alkaline electrolyte gelling agent is investigated. Zinc-air cells are fabricated employing 12 wt.% KOH electrolyte immobilised with hydroponics gel. The cells are discharged at constant currents of 5, 50 and 100 mA. XRD and SEM analysis of the anode plates after discharge show that the failure mode is due to the formation of zinc oxide insulating layers and not due to any side reactions between the gel and the plate or the electrolyte.

Spatially resolved speckle-correlometry of sol-gel transition

NASA Astrophysics Data System (ADS)

Isaeva, A. A.; Isaeva, E. A.; Pantyukov, A. V.; Zimnyakov, D. A.

2018-04-01

Sol-gel transition was studied using the speckle correlometry method with a localized light source and spatial filtering of backscattered radiation. Water solutions of technical or food gelatin with added TiO2 nanoparticles were used as studied objects. Structural transformation of "sol-gel" system was studied at various temperatures from 25°C to 50°C using analysis of the correlation and structure functions of speckle intensity fluctuations. The characteristic temperatures of "sol - gel" transition were evaluated for studied systems. Obtained results can be used for various applications in biomedicine and food industry.

Mechano-responsive hydrogels crosslinked by reactive block copolymer micelles

NASA Astrophysics Data System (ADS)

Xiao, Longxi

Hydrogels are crosslinked polymeric networks that can swell in water without dissolution. Owing to their structural similarity to the native extracelluar matrices, hydrogels have been widely used in biomedical applications. Synthetic hydrogels have been designed to respond to various stimuli, but mechanical signals have not incorporated into hydrogel matrices. Because most tissues in the body are subjected to various types of mechanical forces, and cells within these tissues have sophisticated mechano-transduction machinery, this thesis is focused on developing hydrogel materials with built-in mechano-sensing mechanisms for use as tissue engineering scaffolds or drug release devices. Self-assembled block copolymer micelles (BCMs) with reactive handles were employed as the nanoscopic crosslinkers for the construction of covalently crosslinked networks. BCMs were assembled from amphiphilic diblock copolymers of poly(n-butyl acrylate) and poly(acrylic acid) partially modified with acrylate. Radical polymerization of acrylamide in the presence of micellar crosslinkers gave rise to elastomeric hydrogels whose mechanical properties can be tuned by varying the BCM composition and concentration. TEM imaging revealed that the covalently integrated BCMs underwent strain-dependent reversible deformation. A model hydrophobic drug, pyrene, loaded into the core of BCMs prior to the hydrogel formation, was dynamically released in response to externally applied mechanical forces, through force-induced reversible micelle deformation and the penetration of water molecules into the micelle core. The mechano-responsive hydrogel has been studied for tissue repair and regeneration purposes. Glycidyl methacrylate (GMA)-modified hyaluronic acid (HA) was photochemically crosslinked in the presence of dexamethasone (DEX)-loaded crosslinkable BCMs. The resultant HA gels (HAxBCM) contain covalently integrated micellar compartments with DEX being sequestered in the hydrophobic core. Compared to the traditional HA gels prepared by radical crosslinking of HAGMA, HAxBCM gels exhibited improved drug loading and release capacity. Moreover, compressive forces exerted on the gels were transmitted to the crosslinked BCMs, resulting in a force-modulated DEX release on demand. Micelle mobility in the crosslinked networks was analyzed by fluorescence correlation spectroscopy using nile red loaded BCMs. The anti-inflammatory activities of DEX-releasing HAxBCM gels were evaluated via the in vitro culture of lipopolysaccharide-activated macrophages.

An invasive plant alters pollinator-mediated phenotypic selection on a native congener.

PubMed

Beans, Carolyn M; Roach, Deborah A

2015-01-01

• Recent studies suggest that invasive plants compete reproductively with native plants by reducing the quantity or quality of pollinator visits. Although these studies have revealed ecological consequences of pollinator-mediated competition between invasive and native plants, the evolutionary outcomes of these interactions remain largely unexplored.• We studied the ecological and evolutionary impact of pollinator-mediated competition with an invasive jewelweed, Impatiens glandulifera, on a co-occurring native congener, I. capensis. Using a pollinator choice experiment, a hand pollination experiment, and a selection analysis, we addressed the following questions: (1) Do native pollinators show preference for the invasive or native jewelweed, and do they move between the two species? (2) Does invasive jewelweed pollen inhibit seed production in the native plant? (3) Does the invasive jewelweed alter phenotypic selection on the native plant's floral traits?• The pollinator choice experiment showed that pollinators strongly preferred the invasive jewelweed. The hand pollination experiment demonstrated that invasive pollen inhibited seed production in the native plant. The selection analysis showed that the presence of the invasive jewelweed altered phenotypic selection on corolla height in the native plant.• Invasive plants have the potential to alter phenotypic selection on floral traits in native plant populations. If native plants can evolve in response to this altered selection pressure, the evolution of floral traits may play an important role in permitting long-term coexistence of native and invasive plants. © 2015 Botanical Society of America, Inc.

Hydroxyapatite, fluor-hydroxyapatite and fluorapatite produced via the sol-gel method: bonding to titanium and scanning electron microscopy.

PubMed

Tredwin, Christopher J; Georgiou, George; Kim, Hae-Won; Knowles, Jonathan C

2013-05-01

Hydroxyapatite (HA), fluor-hydroxyapatite (FHA) with varying levels of fluoride ion substitution and fluorapatite (FA) production has been characterised and optimised by the sol-gel method and the dissolution and biological properties of these materials were investigated. It was the objective of this study to investigate the potential bond strength and interaction of these materials with titanium. HA, FHA and FA were synthesised by a sol-gel method. Calcium nitrate and triethyl phosphite were used as precursors under an ethanol-water based solution. Different amounts of ammonium fluoride (NH4F) were incorporated for the preparation of the FHA and FA sol-gels. Using a spin coating technique the sol-gels were coated onto commercially pure titanium disks and crystallised at various temperatures. Using scanning electron microscopy (SEM) and elemental analysis, the surface characteristics, coating thickness and interaction of the Ti substrate and coating were investigated. The bond strengths of the coating to the Ti were investigated using an Instron Universal Load Testing Machine. Statistical analysis was performed with a two-way analysis of variance and post hoc testing with a Bonferroni correction. (1) Coating speed inversely influenced the coating thickness. (2) Increasing fluoride ion substitution and heating temperature significantly increased bond strength and (3) increasing fluoride ion substitution increased the coating thickness. FHA and FA synthesised using the sol-gel technique may offer a superior alternative to coating titanium implants with HA and plasma spraying. HA, FHA and FA materials synthesised by the sol-gel method may also have a use as bone grafting materials. Copyright © 2013 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Analysis of Lipid Phase Behavior and Protein Conformational Changes in Nanolipoprotein Particles upon Entrapment in Sol–Gel-Derived Silica

PubMed Central

2015-01-01

The entrapment of nanolipoprotein particles (NLPs) and liposomes in transparent, nanoporous silica gel derived from the precursor tetramethylorthosilicate was investigated. NLPs are discoidal patches of lipid bilayer that are belted by amphiphilic scaffold proteins and have an average thickness of 5 nm. The NLPs in this work had a diameter of roughly 15 nm and utilized membrane scaffold protein (MSP), a genetically altered variant of apolipoprotein A-I. Liposomes have previously been examined inside of silica sol–gels and have been shown to exhibit instability. This is attributed to their size (∼150 nm) and altered structure and constrained lipid dynamics upon entrapment within the nanometer-scale pores (5–50 nm) of the silica gel. By contrast, the dimensional match of NLPs with the intrinsic pore sizes of silica gel opens the possibility for their entrapment without disruption. Here we demonstrate that NLPs are more compatible with the nanometer-scale size of the porous environment by analysis of lipid phase behavior via fluorescence anisotropy and analysis of scaffold protein secondary structure via circular dichroism spectroscopy. Our results showed that the lipid phase behavior of NLPs entrapped inside of silica gel display closer resemblance to its solution behavior, more so than liposomes, and that the MSP in the NLPs maintain the high degree of α-helix secondary structure associated with functional protein–lipid interactions after entrapment. We also examined the effects of residual methanol on lipid phase behavior and the size of NLPs and found that it exerts different influences in solution and in silica gel; unlike in free solution, silica entrapment may be inhibiting NLP size increase and/or aggregation. These findings set precedence for a bioinorganic hybrid nanomaterial that could incorporate functional integral membrane proteins. PMID:25062385

Study on the rheological properties and volatile release of cold-set emulsion-filled protein gels.

PubMed

Mao, Like; Roos, Yrjö H; Miao, Song

2014-11-26

Emulsion-filled protein gels (EFP gels) were prepared through a cold-set gelation process, and they were used to deliver volatile compounds. An increase in the whey protein isolate (WPI) content from 4 to 6% w/w did not show significant effect on the gelation time, whereas an increase in the oil content from 5 to 20% w/w resulted in an earlier onset of gelation. Gels with a higher WPI content had a higher storage modulus and water-holding capacity (WHC), and they presented a higher force and strain at breaking, indicating that a more compact gel network was formed. An increase in the oil content contributed to gels with a higher storage modulus and force at breaking; however, this increase did not affect the WHC of the gels, and gels with a higher oil content became more brittle, resulting in a decreased strain at breaking. GC headspace analysis showed that volatiles released at lower rates and had lower air-gel partition coefficients in EFP gels than those in ungelled counterparts. Gels with a higher WPI content had lower release rates and partition coefficients of the volatiles. A change in the oil content significantly modified the partition of volatiles at equilibrium, but it produced a minor effect on the release rate of the volatiles. The findings indicated that EFP gels could be potentially used to modulate volatile release by varying the rheological properties of the gel.

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

PubMed

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

2012-01-01

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

Study of low-velocity impact response of sandwich panels with shear-thickening gel cores

NASA Astrophysics Data System (ADS)

Wang, Yunpeng; Gong, Xinglong; Xuan, Shouhu

2018-06-01

The low-velocity impact response of sandwich panels with shear-thickening gel cores was studied. The impact tests indicated that the sandwich panels with shear-thickening gel cores showed excellent properties of energy dissipation and stress distribution. In comparison to the similar sandwich panels with chloroprene rubber cores and ethylene-propylene-diene monomer cores, the shear-thickening gel cores led to the obviously smaller contact forces and the larger energy absorptions. Numerical modelling with finite element analysis was used to investigate the stress distribution of the sandwich panels with shear-thickening gel cores and the results agreed well with the experimental results. Because of the unique mechanical property of the shear-thickening gel, the concentrated stress on the front facesheets were distributed to larger areas on the back facesheets and the peak stresses were reduced greatly.

Immobilization of Chlorosulfonyl-Calix[4]arene onto the surface of silica gel through the directly estrification

NASA Astrophysics Data System (ADS)

Taghvaei-Ganjali, Saeed; Zadmard, Reza; Saber-Tehrani, Mandana

2012-06-01

For the first time Chlorosulfonyl-Calix[4]arene has been chemically bonded to silica gel through the directly estrification without silane coupling agent to prepare Chlorosulfonyl-Calix[4]arene-bonded silica gel. Sample characterization was performed by various techniques such as elemental analysis, Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDAX), powder X-ray diffraction (XRD), N2 adsorption-desorption, thermal gravimetric analysis (TGA), 29Si CP/MAS spectroscopy and acid-base titration. All data approve the successful incorporation of organic group via covalent bond. From the comparison between sulfur content determined by elemental analysis and the number of H+ determined by acid-base titration, it was shown that two ester units took place onto the new synthesized sample and two acidic sites exist on the surface.

Initial experiments with gel-water: towards MRI-linac dosimetry and imaging.

PubMed

Alnaghy, Sarah J; Gargett, Maegan; Liney, Gary; Petasecca, Marco; Begg, Jarrad; Espinoza, Anthony; Newall, Matthew K; Duncan, Mitchell; Holloway, Lois; Lerch, Michael L F; Lazea, Mircea; Rosenfeld, Anatoly B; Metcalfe, Peter

2016-12-01

Tracking the position of a moving radiation detector in time and space during data acquisition can replicate 4D image-guided radiotherapy (4DIGRT). Magnetic resonance imaging (MRI)-linacs need MRI-visible detectors to achieve this, however, imaging solid phantoms is an issue. Hence, gel-water, a material that provides signal for MRI-visibility, and which will in future work, replace solid water for an MRI-linac 4DIGRT quality assurance tool, is discussed. MR and CT images of gel-water were acquired for visualisation and electron density verification. Characterisation of gel-water at 0 T was compared to Gammex-RMI solid water, using MagicPlate-512 (M512) and RMI Attix chamber; this included percentage depth dose, tissue-phantom ratio (TPR 20/10 ), tissue-maximum ratio (TMR), profiles, output factors, and a gamma analysis to investigate field penumbral differences. MR images of a non-powered detector in gel-water demonstrated detector visualisation. The CT-determined gel-water electron density agreed with the calculated value of 1.01. Gel-water depth dose data demonstrated a maximum deviation of 0.7% from solid water for M512 and 2.4% for the Attix chamber, and by 2.1% for TPR 20/10 and 1.0% for TMR. FWHM and output factor differences between materials were ≤0.3 and ≤1.4%. M512 data passed gamma analysis with 100% within 2%, 2 mm tolerance for multileaf collimator defined fields. Gel-water was shown to be tissue-equivalent for dosimetry and a feasible option to replace solid water.

Histological analysis of effects of 24% EDTA gel for nonsurgical treatment of periodontal tissues.

PubMed

de Vasconcellos, Luana Marotta Reis; Ricardo, Lucilene Hernandes; Balducci, Ivan; de Vasconcellos, Luis Gustavo Oliveira; Carvalho, Yasmin Rodarte

2006-12-01

The aim of this study was to investigate, by means of histological and histomorphometric analysis, the effects of 24% ethylenediaminetetraacetic acid (EDTA) gel in periodontal tissue when used in combination with conventional periodontal treatment. Periodontitis was induced in the 2nd upper left permanent molars of 45 male Wistar rats by means of ligature. After 5 weeks, this was removed and debridement was performed. The animals were then randomly divided into 3 groups; group 1: mechanical treatment, group 2: mechanical treatment and EDTA gel application for 2 min, and group 3: mechanical treatment and placebo gel application for 2 min. After the treatment, rinsing was done with 0.9% saline solution for 1 min in all cases, followed by root notching in the deepest part of the pocket. After 4, 10, and 28 days the animals were sacrificed. The averages obtained were evaluated by means of test two-way analysis of variance (ANOVA) and Tukey statistical tests (P < 0.05). The results showed that with respect to the type of treatment employed, there were no statistically significant differences in the vitality of the periodontal tissue. It was concluded that 24% EDTA gel did not interfere with periodontal tissue repair when used in combination with conventional periodontal treatment.

Application of 2-dimensional difference gel electrophoresis (2D-DIGE) to the study of thrombin-activated human platelet secretome.

PubMed

Della Corte, Anna; Maugeri, Norma; Pampuch, Agnieszka; Cerletti, Chiara; de Gaetano, Giovanni; Rotilio, Domenico

2008-02-01

Thrombin is an agonist inducing platelet activation. We combined two-dimensional difference gel electrophoresis (2D-DIGE) and mass spectrometry (MALDI-TOF MS) to analyse differentially expressed proteins secreted from thrombin-stimulated platelets. Human washed platelets, from healthy volunteers, were stimulated with thrombin 0.5 U/ml at 37 degrees C without stirring and the secreted proteins were resolved by 2D-DIGE. By image analysis, 1094 spots were detected in the 2D gel. The spots whose mean intensity showed at least a five-fold change intensity increase or decrease in the thrombin-activated platelet gel in comparison with unstimulated control were digested by trypsin and subjected to MALDI-TOF MS analysis. Peptides from mass spectra of in-gel digest samples were matched against available databases, using the Mascot search engine (Matrix Science) for peptide mass fingerprint. In the activated platelet secretome, transferrin, glutathione-transferase, WD repeat protein, ER-60, thrombospondin-1 precursor and thrombospondin were the most abundant. Also lamin A, a nuclear protein, not previously identified in platelets, appeared to be released. The novel strategy to combine 2D-DIGE with MALDI-TOF MS is a useful approach for a quantitative analysis of the effect of thrombin on the secretome profile of human platelets.

Transfer printing of thermoreversible ion gels for flexible electronics.

PubMed

Lee, Keun Hyung; Zhang, Sipei; Gu, Yuanyan; Lodge, Timothy P; Frisbie, C Daniel

2013-10-09

Thermally assisted transfer printing was employed to pattern thin films of high capacitance ion gels on polyimide, poly(ethylene terephthalate), and SiO2 substrates. The ion gels consisted of 20 wt % block copolymer poly(styrene-b-ethylene oxide-b-styrene and 80 wt % ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethyl sulfonyl)amide. Patterning resolution was on the order of 10 μm. Importantly, ion gels containing the block polymer with short PS end blocks (3.4 kg/mol) could be transfer-printed because of thermoreversible gelation that enabled intimate gel-substrate contact at 100 °C, while gels with long PS blocks (11 kg/mol) were not printable at the same temperature due to poor wetting contact between the gel and substrates. By using printed ion gels as high-capacitance gate insulators, electrolyte-gated thin-film transistors were fabricated that operated at low voltages (<1 V) with high on/off current ratios (∼10(5)). Statistical analysis of carrier mobility, turn-on voltage, and on/off ratio for an array of printed transistors demonstrated the excellent reproducibility of the printing technique. The results show that transfer printing is an attractive route to pattern high-capacitance ion gels for flexible thin-film devices.

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

PubMed

Tietz, D; Gombocz, E; Chrambach, A

1991-10-01

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

Changes in the myosin secondary structure and shrimp surimi gel strength induced by dense phase carbon dioxide.

PubMed

Guo, Minghui; Liu, Shucheng; Ismail, Marliya; Farid, Mohammed M; Ji, Hongwu; Mao, Weijie; Gao, Jing; Li, Chengyong

2017-07-15

Dense phase carbon dioxide (DPCD) could induce protein conformation changes. Myosin and shrimp surimi from Litopenaeus vannamei were treated with DPCD at 5-25MPa and 40-60°C for 20min. Myosin secondary structure was investigated by circular dichroism and shrimp surimi gel strength was determined using textural analysis to develop correlations between them. DPCD had a greater effect on secondary structure and gel strength than heating. With increasing pressure and temperature, the α-helix content of DPCD-treated myosin decreased, while the β-sheet, β-turn and random coil contents increased, and the shrimp surimi gel strength increased. The α-helix content was negatively correlated with gel strength, while the β-sheet, β-turn and random coil contents were positively correlated with gel strength. Therefore, when DPCD induced myosin to form a gel, the α-helix of myosin was unfolded and gradually converted to a β-sheet. Such transformations led to protein-protein interactions and cross-linking, which formed a three-dimensional network to enhance the gel strength. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gel-like properties of MCM-41 material and its transformation to MCM-50 in a caustic alkaline surround

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

Saputra, Hens; Othman, Raihan, E-mail: raihan@iium.edu.my; Sutjipto, A.G.E.

2012-03-15

Highlights: Black-Right-Pointing-Pointer MCM-41 material transforms gradually into MCM-50 lamellar gel upon controlled exposure to 6 M KOH. Black-Right-Pointing-Pointer The formation of MCM-50 ordered gel structure occurs at KOH weight content of 40-70 wt. %. Black-Right-Pointing-Pointer MCM gel phase shows pseudoplastic behavior and possesses homogeneous matrix texture. -- Abstract: MCM-41 material, prepared by sol-gel method, reveals gel-like properties in a caustic alkaline environment, i.e., 6 M potassium hydroxide (KOH) electrolyte. The gellation of MCM-41 starts at a KOH weight ratio of 40 wt.%. The structural change of the material is verified with X-Ray diffractograms and supported by observation using Scanning Electronmore » Microscope (SEM). As the KOH weight ratio increases, the MCM-41 hexagonal arrays structure gradually transforms into MCM-50 lamellar structure before disappearing completely at 80 wt.% KOH. The MCM gel phase is further characterized by rotational viscometry and texture analysis. The gel phase shows shear thinning or pseudoplastic behavior and possesses homogeneous matrix structure.« less

Quality change of apple slices coated with Aloe vera gel during storage.

PubMed

Song, Hye-Yeon; Jo, Wan-Shin; Song, Nak-Bum; Min, Sea C; Song, Kyung Bin

2013-06-01

Fresh-cut apples are easily susceptible to browning and microbial spoilage. In this study, an edible coating prepared from Aloe vera gel containing antibrowning solution was applied to preserve the quality of fresh-cut apples during storage. Fresh-cut apples were treated with both an Aloe vera gel and an Aloe vera gel containing 0.5% cysteine and then stored at 4 °C for 16 d. The color, firmness, weight loss, soluble solid content, titratable acidity, microbial analysis, and sensory evaluation were analyzed during storage. Fresh-cut apples coated with the Aloe vera gel showed delayed browning and reduced weight loss and softening compared to the control. The Aloe vera gel coating was also effective in reducing the populations of the total aerobic bacteria and yeast and molds. In particular, Aloe vera gel containing 0.5% cysteine was most effective in delaying browning and the reduction of microbial populations among the treatments. These results suggest that an Aloe vera gel coating can be used for maintaining the quality of fresh-cut apples. © 2013 Institute of Food Technologists®

Analysis of the SNPforID 52-plex markers in four Native American populations from Venezuela.

PubMed

Ruiz, Y; Chiurillo, M A; Borjas, L; Phillips, C; Lareu, M V; Carracedo, Á

2012-09-01

The SNPforID 52-plex single nucleotide polymorphisms (SNPs) were analyzed in four native Venezuelan populations: Bari, Pemon, Panare and Warao. None of the population-locus combinations showed significant departure from Hardy-Weinberg equilibrium. Calculation of forensic and statistical parameters showed lower values of genetic diversity in comparison with African and European populations, as well as other, admixed populations of neighboring regions of Caribbean, Central and South America. Significant levels of divergence were observed between the four Native Venezuelan populations as well as with other previously studied populations. Analysis of the 52-plex SNP loci with Structure provided an optimum number of population clusters of three, corresponding to Africans, Europeans and Native Americans. Analysis of admixed populations indicated a range of membership proportions for ancestral populations consisting of Native American, African and European components. The genetic differences observed in the Native American groups suggested by the 52 SNPs typed in our study are in agreement with current knowledge of the demographic history of the Americas. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Characterization of partially hydrolyzed OCP crystals deposited in a gelatin matrix as a scaffold for bone tissue engineering

NASA Astrophysics Data System (ADS)

Ezoe, Yushi; Anada, Takahisa; Yamazaki, Hajime; Handa, Takuto; Kobayashi, Kazuhito; Takahashi, Tetsu; Suzuki, Osamu

2015-03-01

The present study was designed to investigate how hydrolysis of octacalcium phosphate (OCP) into hydroxyapatite is affected by the presence of gelatin (Gel) molecules and how osteoblastic cells respond to the resultant OCP hydrolyzate/Gel composites as the hydrolysis advances. OCP was prepared from a solution containing calcium and phosphate ions and Gel molecules, having a composition to produce a 40 wt% OCP as a final co-precipitate as the OCP/Gel. The precipitate was further incubated up to 40 h to advance the hydrolysis of OCP. These precipitates were processed to mold OCP/Gel sponges through lyophilization and dehydrothermal treatment. Chemical analysis, X-ray diffraction, Fourier transform infrared spectroscopy, transmission electron microscopy, and selected area electron diffraction revealed that the hydrolysis of OCP/Gel composite in hot water advanced in a time-dependent manner and faster than hydrolysis of OCP alone. The effect of Gel on the OCP hydrolysis was further examined in the presence of distinct concentrations of Gel molecules in hot water, showing that the Gel enhanced the hydrolysis as the concentration increased. Proliferation and differentiation of mouse bone marrow stromal ST-2 cells on the hydrolyzed OCP/Gel composites were compatible with Gel sponge alone after 21 days of culture, suggesting that these composites could be a candidate as a scaffold in bone tissue engineering.

Unravelling the differences: comparative proteomic analysis of a clonal virulent and an attenuated Histomonas meleagridis strain.

PubMed

Monoyios, Andreas; Patzl, Martina; Schlosser, Sarah; Hess, Michael; Bilic, Ivana

2018-02-01

The current study focused on Histomonas meleagridis, a unicellular protozoan, responsible for histomonosis in poultry. Recently, the occurrence of the disease increased due to the ban of effective chemotherapeutic drugs. Basic questions regarding the molecular biology, virulence mechanisms or even life cycle of the flagellate are still puzzling. In order to address some of these issues, we conducted a comparative proteomic analysis of a virulent and an attenuated H. meleagridis strain traced back to a single cell and propagated in vitro as monoxenic mono-eukaryotic cultures. Using two-dimensional electrophoresis (2-DE) for proteome visualization with computational 2-DE gel image and statistical analysis, upregulated proteins in either of the two H. meleagridis strains were detected. Statistical analysis fulfilling two criteria (≥threefold upregulation and P < 0.05) revealed 119 differentially expressed protein spots out of which 62 spots were noticed in gels with proteins from the virulent and 57 spots in gels with proteins from the attenuated culture. Mass spectrometric analysis of 32 protein spots upregulated in gels of the virulent strain identified 17 as H. meleagridis-specific. The identification revealed that these spots belonged to eight different proteins, with the majority related to cellular stress management. Two ubiquitous cellular proteins, actin and enolase, were upregulated in multiple gel positions in this strain, indicating either post-translational modification or truncation, or even both. Additionally, a known virulence factor named legumain cysteine peptidase was also detected. In contrast to this, mass spectrometric analysis of 49 protein spots, upregulated in gels of the attenuated strain, singled out 32 spots as specific for the flagellate. These spots were shown to correspond to 24 different proteins that reflect the increased metabolism, in vitro adaptation of the parasite, and amoeboid morphology. In addition to H. meleagridis proteins, the analysis identified differential expression of Escherichia coli DH5α proteins that could have been influenced by the co-cultivated H. meleagridis strain, indicating a reciprocal interaction of these two organisms during monoxenic cultivation. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

2D-DIGE proteomic analysis of mesenchymal stem cell cultured on the elasticity-tunable hydrogels.

PubMed

Kuboki, Thasaneeya; Kantawong, Fahsai; Burchmore, Richard; Dalby, Matthew J; Kidoaki, Satoru

2012-01-01

The present study focuses on mechanotransduction in mesenchymal stem cells (MSCs) in response to matrix elasticity. By using photocurable gelatinous gels with tunable stiffness, proteomic profiles of MSCs cultured on tissue culture plastic, soft (3 kPa) and stiff (52 kPa) matrices were deciphered using 2-dimensional differential in-gel analysis (2D-DIGE). The DIGE data, tied to immunofluorescence, indicated abundance and organization changes in the cytoskeletonal proteins as well as differential regulation of important signaling-related proteins, stress-responsing proteins and also proteins involved in collagen synthesis. The major CSK proteins including actin, tubulin and vimentin of the cells cultured on the gels were remarkably changed their expressions. Significant down-regulation of α-tubulin and β-actin can be observed on gel samples in comparison to the rigid tissue culture plates. The expression abundance of vimentin appeared to be highest in the MSCs cultured on hard gels. These results suggested that the substrate stiffness significantly affects expression balances in cytoskeletal proteins of MSCs with some implications to cellular tensegrity.

Alterations in brain cerebral cortex proteome of rabies-infected cat.

PubMed

Kasempimolporn, Songsri; Lumlertdacha, Boonlert; Chulasugandha, Pannipa; Boonchang, Supatsorn; Sitprija, Visith

2014-07-01

Comparative proteome analysis using brain cerebral cortex tissues from cats and dogs infected with/without rabies virus were conducted using both two-dimensional gel-electrophoresis (2-DE) and 2-D fluorescence difference gel- electrophoresis (2D-DIGE) methods. The 2-DE gel images of all samples revealed >1,000 protein spots in each gel. Quantitative intensity analysis revealed the same overall protein pattern in certain regions of the gel, but the rabies-infected brains exhibited more protein spots than the non-infected controls. From approximately 880 protein spots detected by 2D-DIGE, 65 protein spots were increased and 46 were decreased. Eight of these protein spots were randomly selected and annotated by reference to previous known proteome data of rabid dog brains. They were similarly altered in both of the rabies-infected cats and dogs. A more detailed comparison of changes in proteomic profiles of brains between rabid cats and dogs should shed some light on the pathophysiological mechanism of rabies in domestic animals, as most rabies cases have been traceable to or believed to have originated from rabid dogs.

Low temperature synthesis of monolithic transparent Ta2O5 gels from hydrolysis of metal alkoxide

NASA Technical Reports Server (NTRS)

Bansal, Narottam P.

1993-01-01

Tantalum oxide gels in the form of transparent monoliths and powder were prepared from hydrolysis of tantalum pentaethoxide under controlled conditions using different mole ratios of Ta(OC2H5)5:C2H50H:H20:HCl. Alcohol acts as the mutual solvent and HCl as the deflocculating agent. For a fixed alkoxide:water:HCl ratio, time of gel formation increased with the alcohol to alkoxide mole ratio. Thermal evolution of the physical and structural changes in the gel was monitored by differential thermal analysis, thermogravimetric analysis, x-ray diffraction, and infrared spectroscopy. On heating to approximately 400 C, the amorphous gel crystallized into the low temperature orthorhombic phase Beta-Ta2O5, which transformed into the high temperature tetragonal phase Alpha-Ta2O5 when further heated to approximately 1450 C. The volume fraction of the crystalline phase increased with the firing temperature. The Alpha-Ta205 converted back into the low temperature phase, Beta-Ta2O5, on slow cooling through the transformation temperature of 1360 C indicating a slow but reversible transformation.

Effect of belimbing wuluh (averrhoa bilimbi l.) extract gel exposure duration to surface roughness of enamel

NASA Astrophysics Data System (ADS)

Karima, F.; Eriwati, Y. K.; Triaminingsih, S.

2017-08-01

The purpose of this study was to analyze the effect of Belimbing Wuluh Gel Extract to surface roughness of enamel. Thirty-six premolars teeth that divided into 4 groups (n = 9), were exposed to 37% phosphoric acid gel (pH = 1) for 15 seconds as a control group, and belimbing wuluh extract gel with a concentration of 80% (pH = 1.8) for 15 seconds, 20 seconds, and 25 seconds as the treatment groups. The statistical analysis of paired and unpaired T-test shows that all treatment groups experienced a significant change (p <0.05). The greatest changes in surface roughness of enamel occurred after exposed by belimbing extract gel with an exposure duration of 25 seconds, but the roughness of 37% phosphoric acid gel is still greater. There was a correlation between roughness on the surface of tooth enamel with prolonged exposure belimbing wuluh extract gel with a concentration of 80%.

PREPARATION AND PROPERTIES OF COMPOUND ARNEBIAE RADIX MICROEMULSION GEL

PubMed Central

Chen, Jing; He, Yanping; Gao, Ting; Zhang, Licheng; Zhao, Yuna

2017-01-01

Background: Compound Arnebiae radix oil has been clinically applied to treat burns and scalds for a long time. However, it is unstable and inconvenient to use. The aim of this study was to prepare a compound Arnebiae radix microemulsion gel for transdermal delivery system and evaluate its characteristics. Materials and Methods: Based on the solubility of Shikonin, the active component of Arnebiae radix and the results of phase studies, adequate ratio of each component in microemulsion was determined. The optimized microemulsion gel was prepared using Carbomer 940. The gels were characterized in terms of appearance, preliminary stability test and the content of Shikonin in the compound Arnebiae radix microemulsion gel with HPLC analysis. Results: The optimized conditions for preparing microemulsion were Tween-80, glycerin, isopropyl myristate (IPM) with the ratio of 6:3:2. The optimal microemulsion gel was obtained with Carbomer 940 (1.0%). Conclusion: The prepared compound Arnebiae radix microemulsion gel showed good stability over time. It is more convenience in application than the previous used formulations. PMID:28480438

PREPARATION AND PROPERTIES OF COMPOUND ARNEBIAE RADIX MICROEMULSION GEL.

PubMed

Chen, Jing; He, Yanping; Gao, Ting; Zhang, Licheng; Zhao, Yuna

2017-01-01

Compound Arnebiae radix oil has been clinically applied to treat burns and scalds for a long time. However, it is unstable and inconvenient to use. The aim of this study was to prepare a compound Arnebiae radix microemulsion gel for transdermal delivery system and evaluate its characteristics. Based on the solubility of Shikonin, the active component of Arnebiae radix and the results of phase studies, adequate ratio of each component in microemulsion was determined. The optimized microemulsion gel was prepared using Carbomer 940. The gels were characterized in terms of appearance, preliminary stability test and the content of Shikonin in the compound Arnebiae radix microemulsion gel with HPLC analysis. The optimized conditions for preparing microemulsion were Tween-80, glycerin, isopropyl myristate (IPM) with the ratio of 6:3:2. The optimal microemulsion gel was obtained with Carbomer 940 (1.0%). The prepared compound Arnebiae radix microemulsion gel showed good stability over time. It is more convenience in application than the previous used formulations.

Ferroelectric and piezoelectric properties of poly(vinylidene fluoride-trifluoroethylene) gels

NASA Astrophysics Data System (ADS)

Fukagawa, Miki; Koshiba, Yausko; Morimoto, Masahiro; Ishida, Kenji

2017-04-01

The structural, ferroelectric, and piezoelectric properties of poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] gels fabricated using poly(pyridinium-1,4-diyliminocarbonyl-1,4-phenylenemethylene thiocyanate) (PICPM-SCN) as a gelator are investigated in this study. The P(VDF-TrFE)/PICPM-SCN composites formed thermally reversible physical gels and their analysis by Fourier transform infrared spectroscopy revealed that the P(VDF-TrFE) molecules in these gels exhibit predominantly the ferroelectric phase I (Form β). Furthermore, the polarization switching peaks of the P(VDF-TrFE)/PICPM-SCN gel films were clearly observed. The coercive electric field for these gel films was estimated to be 2 MV/m, which is dramatically lower than the values typically observed for P(VDF-TrFE) solid films (50 MV/m). Finally, the P(VDF-TrFE)/PICPM-SCN gel films exhibited a piezoelectric response, and the highest piezoelectric coefficient was determined to be ˜53 pm/V at an applied voltage frequency of 4 kHz.

Advances in native high-performance liquid chromatography and intact mass spectrometry for the characterization of biopharmaceutical products.

PubMed

Tassi, Marco; De Vos, Jelle; Chatterjee, Sneha; Sobott, Frank; Bones, Jonathan; Eeltink, Sebastiaan

2018-01-01

The characterization of biotherapeutics represents a major analytical challenge. This review discusses the current state-of-the-art in analytical technologies to profile biopharma products under native conditions, i.e., the protein three dimensional conformation is maintained during liquid chromatographic analysis. Native liquid-chromatographic modes that are discussed include aqueous size-exclusion chromatography, hydrophobic interaction chromatography, and ion-exchange chromatography. Infusion conditions and the possibilities and limitations to hyphenate native liquid chromatography to mass spectrometry are discussed. Furthermore, the applicability of native liquid-chromatography methods and intact mass spectrometry analysis for the characterization of monoclonal antibodies and antibody-drug conjugates is discussed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Purification and characterization of ornithine transcarbamylase from pea (Pisum sativum L.)

NASA Technical Reports Server (NTRS)

Slocum, R. D.; Richardson, D. P.

1991-01-01

Pea (Pisum sativum) ornithine transcarbamylase (OTC) was purified to homogeneity from leaf homogenates in a single-step procedure, using delta-N-(phosphonacetyl)-L-ornithine-Sepharose 6B affinity chromatography. The 1581-fold purified OTC enzyme exhibited a specific activity of 139 micromoles citrulline per minute per milligram of protein at 37 degrees C, pH 8.5. Pea OTC represents approximately 0.05% of the total soluble protein in the leaf. The molecular weight of the native enzyme was approximately 108,200, as estimated by Sephacryl S-200 gel filtration chromatography. The purified protein ran as a single molecular weight band of 36,500 in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These results suggest that the pea OTC is a trimer of identical subunits. The overall amino acid composition of pea OTC is similar to that found in other eukaryotic and prokaryotic OTCs, but the number of arginine residues is approximately twofold higher. The increased number of arginine residues probably accounts for the observed isoelectric point of 7.6 for the pea enzyme, which is considerably more basic than isoelectric point values that have been reported for other OTCs.

Purification and characterization of peroxidase from cauliflower (Brassica oleracea L. var. botrytis) buds.

PubMed

Köksal, Ekrem; Gülçin, Ilhami

2008-01-01

Peroxidases (EC 1.11.1.7; donor: hydrogen peroxide oxidoreductase) are part of a large group of enzymes. In this study, peroxidase, a primer antioxidant enzyme, was purified with 19.3 fold and 0.2% efficiency from cauliflower (Brassica oleracea L.) by ammonium sulphate precipitation, dialysis, CM-Sephadex ion-exchange chromatography and Sephadex G-25 purification steps. The substrate specificity of peroxidase was investigated using 2,2'-azino-bis(3-ethylbenz-thiazoline-6-sulphonic acid) (ABTS), 2-methoxyphenol (guaiacol), 1,2-dihydroxybenzene (catechol), 1,2,3-trihyidroxybenzene (pyrogallol) and 4-methylcatechol. Also, optimum pH, optimum temperature, optimum ionic strength, stable pH, stable temperature, thermal inactivation conditions were determined for guaiacol/H(2)O(2), pyrogallol/H(2)O(2), ABTS/H(2)O(2), catechol/H(2)O(2) and 4-methyl catechol/H(2)O(2) substrate patterns. The molecular weight (M(w)) of this enzyme was found to be 44 kDa by gel filtration chromatography method. Native polyacrylamide gel electrophoresis (PAGE) was performed for isoenzyme determination and a single band was observed. K(m) and V(max) values were calculated from Lineweaver-Burk graph for each substrate patterns.

Enzymatic Properties of an Alkaline and Chelator Resistant alpha-amylase from the Alkaliphilic Bacillus sp. Isolate L1711

NASA Technical Reports Server (NTRS)

Bernhardsdotter, Eva C. M. J.; Pusey, Marc L.; Ng, Joseph D.; Garriott, Owen K.

2004-01-01

An alkaliphilic amylase producing bacterium, Bacillus sp. strain L 711, was selected among 13 soda lakes isolates. When grown at pH 10.5 and 37 C, strain L711 produced multiple forms of amylases in the culture broth. One of these, BAA, was purified from the culture supernatant by QAE column chromatography and preparative native gel electrophoresis. The molecular weight of BAA was determined to be 51 kDa by denaturing gel electrophoresis. The pH optima for activity below and above 40 C were 9.5 - 10.0 and 7.0 - 7.5 respectively. BAA was stable in the pH range 6-11 and was completely inactivated at 55 C. The thermostability was not increased in the presence of Ca(2+). The enzyme was strongly inhibited by Ca(2+), Zn(2+), Mg(2+), Mn(2+), Ba(2+) and Cu(2+), whereas the presence of Na(+), Co(2+) and EDTA (10 mM) enhanced enzymatic activity. The K(sub m), and specific activity of BAA on soluble starch were 1.9 mg/ml and 18.5 U/mg respectively. The main end products of hydrolysis were maltotetraose, maltose and glucose.

Enzymatic Properties of an Alkaline and Chelator Resistant Proportional to alpha-Amylase from the Alkaliphilic Bacillus sp. Isolate L1711

NASA Technical Reports Server (NTRS)

Bernhardsdotter, Eva C. M. J.; Pusey, Marc L.; Ng, Joseph D.; Garriott, Owen K.

2004-01-01

An alkaliphilic amylase producing bacterium, Bacillus sp. strain L1711, was selected among 13 soda lakes isolates. When grown at pH 10.5 and 370 C, strain L1711 produced multiple forms of amylases in the culture broth. One of these, BAA, was purified from the culture supernatant by QAE column chromatography and preparative native gel electrophoresis. The molecular weight of BAA was determined to be 51 kDa by denaturing gel electrophoresis. The pH optima for activity below and above 40 C were 9.5-10.0 and 7.0-7.5 respectively. BAA was stable in the pH range 6-11 and was completely inactivated at 55?C. The thermostability was not increased in the presence of Ca(2+). The enzyme was strongly inhibited by Ca(2+), Zn(2+), Mg(2+), Mn(2+), Ba(2+) and Cu(2+), whereas the presence of Na(+), Co2+ and EDTA (10 mM) enhanced enzymatic activity. The K(sub m) and specific activity of BAA on soluble starch were 1.9 mg/ml and 18.5 U/mg respectively. The main end products of hydrolysis were maltotetraose, maltose and glucose .

Mannan-binding lectin of the sea urchin Strongylocentrotus nudus.

PubMed

Bulgakov, Aleksandr A; Eliseikina, Marina G; Kovalchuk, Svetlana N; Petrova, Irina Yu; Likhatskaya, Galina N; Shamshurina, Ekaterina V; Rasskazov, Valery A

2013-02-01

A novel lectin specific to low-branched mannans (MBL-SN) was isolated from coelomic plasma of the sea urchin Strongylocentrotus nudus by combining anion-exchange liquid chromatography on DEAE Toyopearl 650 M, affinity chromatography on mannan-Sepharose and gel filtration on the Sephacryl S-200. The molecular mass of MBL-SN was estimated by sodium dodecyl sulphate polyacrylamide gel electrophoresis under non-reducing conditions to be about 34 kDa. MBL-SN was shown to be a dimer with two identical subunits of about 17 kDa. The native MBL-SN exists as a tetramer. The physico-chemical properties of MBL-SN indicate that it belongs to C-type mannan-binding lectins. The cDNA encoding MBL-SN was cloned from the total cDNA of S. nudus coelomocytes and encodes a 17-kDa protein of 144 amino acid residues that contains a single carbohydrate-recognition domain of C-type lectins. Prediction of the MBL-SN tertiary structure using comparative modelling revealed that MBL-SN is an α/β-protein with eight β-strands and two α-helices. Comparison of the MBL-SN model with available three-dimensional structures of C-type lectins revealed that they share a common fold pattern.

Red blood cells release factors with growth and survival bioactivities for normal and leukemic T cells.

PubMed

Antunes, Ricardo F; Brandão, Cláudia; Maia, Margarida; Arosa, Fernando A

2011-01-01

Human red blood cells are emerging as a cell type capable to regulate biological processes of neighboring cells. Hereby, we show that human red blood cell conditioned media contains bioactive factors that favor proliferation of normal activated T cells and leukemic Jurkat T cells, and therefore called erythrocyte-derived growth and survival factors. Flow cytometry and electron microscopy in parallel with bioactivity assays revealed that the erythrocyte factors are present in the vesicle-free supernatant, which contains up to 20 different proteins. The erythrocyte factors are thermosensitive and do not contain lipids. Native polyacrylamide gel electrophoresis followed by passive elution and mass spectrometry identification reduced the potential erythrocyte factors to hemoglobin and peroxiredoxin II. Two-dimensional differential gel electrophoresis of the erythrocyte factors revealed the presence of multiple hemoglobin oxy-deoxy states and peroxiredoxin II isoforms differing in their isoelectric point akin to the presence of β-globin chains. Our results show that red blood cells release protein factors with the capacity to sustain T-cell growth and survival. These factors may have an unforeseen role in sustaining malignant cell growth and survival in vivo.

Dichloromethane dehalogenase of Hyphomicrobium sp. strain DM2.

PubMed

Kohler-Staub, D; Leisinger, T

1985-05-01

Dichloromethane dehalogenase, a highly inducible glutathione-dependent enzyme catalyzing the conversion of dichloromethane into formaldehyde and inorganic chloride, was purified fivefold with 60% yield from Hyphomicrobium sp. strain DM2. The electrophoretically homogeneous purified enzyme exhibited a specific activity of 17.3 mkat/kg of protein. Its pH optimum was 8.5. The enzyme was stable at -20 degrees C for at least 6 months. A subunit molecular weight of 33,000 was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Gel filtration of native dichloromethane dehalogenase yielded a molecular weight of 195,000. Subunit cross-linking with dimethyl suberimidate confirmed the hexameric tertiary structure of the enzyme. Dichloromethane dehalogenase was highly specific for dihalomethanes. Its apparent Km values were 30 microM for CH2Cl2, 15 microM for CH2BrCl, 13 microM for CH2Br2, 5 microM for CH2I2, and 320 microM for glutathione. Several chlorinated aliphatic compounds inhibited the dichloromethane dehalogenase activity of the pure enzyme. The Ki values of the competitive inhibitors 1,2-dichloroethane and 1-chloropropane were 3 and 56 microM, respectively.

Dichloromethane dehalogenase of Hyphomicrobium sp. strain DM2.

PubMed Central

Kohler-Staub, D; Leisinger, T

1985-01-01

Dichloromethane dehalogenase, a highly inducible glutathione-dependent enzyme catalyzing the conversion of dichloromethane into formaldehyde and inorganic chloride, was purified fivefold with 60% yield from Hyphomicrobium sp. strain DM2. The electrophoretically homogeneous purified enzyme exhibited a specific activity of 17.3 mkat/kg of protein. Its pH optimum was 8.5. The enzyme was stable at -20 degrees C for at least 6 months. A subunit molecular weight of 33,000 was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Gel filtration of native dichloromethane dehalogenase yielded a molecular weight of 195,000. Subunit cross-linking with dimethyl suberimidate confirmed the hexameric tertiary structure of the enzyme. Dichloromethane dehalogenase was highly specific for dihalomethanes. Its apparent Km values were 30 microM for CH2Cl2, 15 microM for CH2BrCl, 13 microM for CH2Br2, 5 microM for CH2I2, and 320 microM for glutathione. Several chlorinated aliphatic compounds inhibited the dichloromethane dehalogenase activity of the pure enzyme. The Ki values of the competitive inhibitors 1,2-dichloroethane and 1-chloropropane were 3 and 56 microM, respectively. Images PMID:3988708

Purification and Characterization of S-Adenosyl-l-Methionine: Desoxyhemigossypol-6-O-Methyltransferase from Cotton Plants. An Enzyme Capable of Methylating the Defense Terpenoids of Cotton1

PubMed Central

Liu, Jinggao; Benedict, Chauncey R.; Stipanovic, Robert D.; Bell, Alois A.

1999-01-01

Cotton contains a unique group of terpenoids including desoxyhemigossypol, hemigossypol, gossypol, hemigossypolone, and the heliocides that are part of the plant's defense system against pathogenic fungi and insects. Desoxyhemigossypol is a key intermediate in the biosynthesis of these compounds. We have isolated, purified, and characterized from cotton stele tissue infected with Verticillium dahliae a methyltransferase (S-adenosyl-l-Met: desoxyhemigossypol-6-O-methyltransferase) that specifically methylates the 6-position of desoxyhemigossypol to form desoxyhemigossypol-6-methyl ether with a Km value of 4.5 μm for desoxyhemigossypol and a Kcat/Km of 5.08 × 104 s−1 (mol/L)−1. The molecular mass of the native enzyme is 81.4 kD and is dissociated into two subunits of 41.2 kD on sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. The enzymatic reaction does not require Mg+2 and is inhibited 98% with 10 mm p-chloromercuribenzoate. Desoxyhemigossypol-6-methyl ether leads to the biosynthesis of methylated hemigossypol, gossypol, hemigossypolone, and the heliocides, which lowers their effectiveness as phytoalexins and insecticides. PMID:10557251

The Diatom Staurosirella pinnata for Photoactive Material Production

PubMed Central

Prosposito, Paolo; Casalboni, Mauro; Lamastra, Francesca Romana; Nanni, Francesca; Congestri, Roberta

2016-01-01

A native isolate of the colonial benthic diatom Staurosirella pinnata was cultivated for biosilica production. The silicified cell walls (frustules) were used as a source of homogeneous and structurally predictable porous biosilica for dye trapping and random laser applications. This was coupled with the extraction of lipids from biomass showing potential to fabricate photoactive composite materials sustainably. The strain was selected for its ease of growth in culture and harvesting. Biosilica and lipids were obtained at the end of growth in indoor photobioreactors. Frustules were structurally characterized microscopically and their chemistry analyzed with Fourier Transform Infrared Spectroscopy. Frustule capacity of binding laser dyes was evaluated on a set of frustules/Rhodamine B (Rho B) solutions and with respect to silicon dioxide and diatomite by Fluorescence Spectroscopy demonstrating a high affinity for the organic dye. The effect of dye trapping property in conveying Rho B emission to frustules, with enhancement of scattering events, was analyzed on Rho B doped polyacrylamide gels filled or not with frustules. Amplified spontaneous emission was recorded at increasing pump power indicating the onset of a random laser effect in frustule filled gels at lower power threshold compared to unfilled matrices. PMID:27828985

Purification and characterization of vanillin dehydrogenases from alkaliphile Micrococcus sp. TA1 and neutrophile Burkholderia cepacia TM1.

PubMed

Mitsui, Ryoji; Hirota, Mizuho; Tsuno, Takuo; Tanaka, Mitsuo

2010-02-01

Vanillin dehydrogenases (VDHs) were purified and characterized from two bacterial strains that have different pH dependencies for growth. The alkaliphile Micrococcus sp. TA1, isolated from an alkaline spa, can grow on several aromatic compounds such as ferulic acid, vanillin, vanillic acid, and protocatechuic acid under alkaline conditions. The neutrophile Burkholderia cepacia TM1, which was isolated previously, also grew on the above-mentioned compounds because they functioned as the sole carbon source under neutral conditions. Purified VDHs showed activities toward some aromatic aldehydes. These enzymes have the same subunit molecular mass of about 57 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but differed in some of their observed properties. Native molecular masses also differed between the purified enzymes. These were 250 kDa for the enzyme from alkaliphilic strain TA1 and 110 kDa for that from neutrophilic strain TM1, as determined by gel filtration. The enzyme from strain TA1 required NADP(+) as a coenzyme for its activity, but that from strain TM1 required NAD(+). These results are important because this is the first report of an alkaliphilic bacterium consuming lignin monomers.

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.

Purification and properties of a novel ferricyanide-linked xanthine dehydrogenase from Pseudomonas putida 40.

PubMed Central

Woolfolk, C A

1985-01-01

The isolation of a xanthine dehydrogenase from Pseudomonas putida 40 which utilizes ferricyanide as an electron acceptor at high efficiency is presented. The new activity is separate from the NAD+ and oxygen-utilizing activities of the same organism but displays a broad pattern for reducing substrates typical of those of previously studied xanthine-oxidizing enzymes. Unlike the previously studied enzymes, the new enzyme appears to lack flavin but possess heme and is resistant to cyanide treatment. However, sensitivity of the purified enzyme to methanol and the selective elimination of the activity when tungstate is added to certain growth media suggest a role for molybdenum. The enzyme is subject to a selective proteolytic action during processing which is not accompanied by denaturation or loss of activity and which is minimized by the continuous exposure of the activity to EDTA and phenylmethylsulfonyl fluoride. Electrophoresis of the denatured enzyme in the presence of sodium dodecyl sulfate suggests that the enzyme is constructed of subunits with a molecular weight of approximately 72,000. Electrophoresis under native conditions of a purified enzyme previously exposed to magnesium ion reveals a series of major and minor activity bands which display some selectivity toward both electron donors and acceptors. An analysis of the effect of gel concentration on this pattern suggests that the enzyme forms a series of charge and size isomers with a pair of trimeric forms predominating. Comparison of the rate of sedimentation of the enzyme in sucrose gradients with its elution profile from standardized Sepharose 6B columns suggests a molecular weight of 255,000 for the major form of the native enzyme. Images PMID:3860496

A low-cost microwell device for high-resolution imaging of neurite outgrowth in 3D

NASA Astrophysics Data System (ADS)

Ren, Yuan; Mlodzianoski, Michael J.; Cheun Lee, Aih; Huang, Fang; Suter, Daniel M.

2018-06-01

Objective. Current neuronal cell culture is mostly performed on two-dimensional (2D) surfaces, which lack many of the important features of the native environment of neurons, including topographical cues, deformable extracellular matrix, and spatial isotropy or anisotropy in three dimensions. Although three-dimensional (3D) cell culture systems provide a more physiologically relevant environment than 2D systems, their popularity is greatly hampered by the lack of easy-to-make-and-use devices. We aim to develop a widely applicable 3D culture procedure to facilitate the transition of neuronal cultures from 2D to 3D. Approach. We made a simple microwell device for 3D neuronal cell culture that is inexpensive, easy to assemble, and fully compatible with commonly used imaging techniques, including super-resolution microscopy. Main results. We developed a novel gel mixture to support 3D neurite regeneration of Aplysia bag cell neurons, a system that has been extensively used for quantitative analysis of growth cone dynamics in 2D. We found that the morphology and growth pattern of bag cell growth cones in 3D culture closely resemble the ones of growth cones observed in vivo. We demonstrated the capability of our device for high-resolution imaging of cytoskeletal and signaling proteins as well as organelles. Significance. Neuronal cell culture has been a valuable tool for neuroscientists to study the behavior of neurons in a controlled environment. Compared to 2D, neurons cultured in 3D retain the majority of their native characteristics, while offering higher accessibility, control, and repeatability. We expect that our microwell device will facilitate a wider adoption of 3D neuronal cultures to study the mechanisms of neurite regeneration.

Cloning, expression and activation of a truncated 92-kDa gelatinase minienzyme.

PubMed

Kröger, M; Tschesche, H

1997-09-01

The matrix metalloproteinases (MMPs) are a family of highly homologous zinc-endopeptidases that degrade extracellular matrix components. Human 92-kDa gelatinase (MMP-9) represents one of the MMPs that cleaves native collagen type IV. As a basis for structural investigations, the short form (catalytic domain, amino acid residues 113-450) of the 92-kDa gelatinase cDNA was cloned and expressed in E. coli as a minienzyme. By combination of reverse transcription (RT) and polymerase chain reaction (PCR), the truncated 92-kDa gelatinase-cDNA was amplified from the corresponding mRNA derived from ovarian carcinoma cells. The cDNA fragment obtained was cloned in E. coli and sequenced. With the exception of one nucleotide inversion at position 745 (gt-->tg) the cDNA sequence was identical to the nucleotide sequence of the 92-kDa gelatinase as has been previously reported. The protein was expressed in E. coli using the vector pET-12b. The recombinant protein was stored in inclusion bodies and extracted as a 38 kDa species from the inclusion bodies by solubilization in 8 M urea. The product was purified by affinity chromatography and gel filtration. Amino-terminal sequence analysis confirmed the identity with the catalytic domain of 92-kDa gelatinase. The recombinant protein was refolded in the presence of Ca2+ and Zn2+ and yielded an active minienzyme with gelatinolytic activity. It degrades the native substrate collagen type IV and the synthetic substrate Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 x AcOH like the full-length 92-kDa gelatinase. The catalytic activity could be inhibited by the specific MMP inhibitors TIMP-1 and TIMP-2.

Oligomeric properties and DNA binding specificities of repressor isoforms from the Streptomyces bacteriophage phiC31.

PubMed

Wilson, S E; Smith, M C

1998-05-15

Three protein isoforms (74, 54 and 42 kDa) are expressed from repressor gene c in the Streptomyces temperate bacteriophage phiC31. Because expression of the two smaller isoforms, 54 and 42 kDa, is sufficient for superinfection immunity, the interaction between these isoforms was studied. The native 42 kDa repressor (Nat42) and an N-terminally 6x histidine-tagged 54 kDa isoform (His54) were shown by co-purification on a Ni-NTA column to interact in Streptomyces lividans . In vitro three repressor preparations, containing Nat42, His54 and the native 54 and 42 kDa isoforms expressed together (Nat54&42), were subjected to chemical crosslinking and gel filtration analysis. Homo- and hetero-tetramers were observed. Previous work showed that the smallest isoform bound to 17 bp operators containing aconservedinvertedrepeat (CIR) and that the CIRs were located at 16 loci throughout the phiC31 genome. One of the CIRs (CIR6) is believed to be critical for regulating the lytic pathway. The DNA binding activities of the three repressor preparations were studied using fragments containing CIRs (CIR3-CIR6) from the essential early region as templates for DNase I footprinting. Whereas Nat42 bound to CIR6, poorly to CIR5 but undetectably to CIR3 or CIR4, the Nat54&42 preparation could bind to all CIRs tested, albeit poorly to CIR3 and CIR4. The His54 isoform bound all CIRs tested. Isoforms expressed from the phiC31 repressor gene, like those which are expressed from many eukaryotic transcription factor genes, apparently have different binding specificities.

Stiparin: a glycoprotein from sea cucumber dermis that aggregates collagen fibrils.

PubMed

Trotter, J A; Lyons-Levy, G; Luna, D; Koob, T J; Keene, D R; Atkinson, M A

1996-07-01

The interactions between collagen fibrils in many echinoderm connective tissues are rapidly altered by the secretions of resident neurosecretory cells. Recent evidence has suggested that a secreted protein is responsible for the interactions that lead to an increase in tissue stiffness (Trotter and Koob, 1995). Structurally intact collagen fibrils have been isolated from such a connective tissue- the dermis of the sea cucumber Cucumaria frondosa- and used in an assay in vitro to identify a protein that binds to them and causes them to aggregate. This protein has been purified by anion-exchange and molecular sieve chromatography. It is eluted from a MonoQ column at approximately 0.55 M NaCl. Its isoelectric point is 5.2. It elutes from a Superose-6 column in a position corresponding to a molecule with a Stokes radius of 11.5 nm. Its native molecular weight estimated from sedimentation equilibrium analysis under non-denaturing conditions is 375,000, and its monomer molecular weight, estimated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, is approximately 350,000. Sedimentation velocity measurements indicated for the native molecule a sedimentation coefficient of 11 x 10(-13)s, a diffusion coefficient of 3.274 x 10(-7) cm2s-1, and a frictional ratio of 1.95, which corresponds to a prolate ellipsoid of revolution with an axial ratio of 19. The highly asymmetric structure suggested by the above correlated well with the images obtained by transmission electron microscopy following rotary shadowing, which revealed a flexible structure approximately 125 nm long. Based on its ability to aggregate collagen fibrils, this protein has been named "stiparin," from the Latin stipare, "to pack together."

Introducing Students to Protein Analysis Techniques: Separation and Comparative Analysis of Gluten Proteins in Various Wheat Strains

ERIC Educational Resources Information Center

Pirinelli, Alyssa L.; Trinidad, Jonathan C.; Pohl, Nicola L. B.

2016-01-01

Polyacrylamide gel electrophoresis (PAGE) is commonly taught in undergraduate laboratory classes as a traditional method to analyze proteins. An experiment has been developed to teach these basic protein gel skills in the context of gluten protein isolation from various types of wheat flour. A further goal is to relate this technique to current…

How to Study Basement Membrane Stiffness as a Biophysical Trigger in Prostate Cancer and Other Age-related Pathologies or Metabolic Diseases

PubMed Central

Rodriguez-Teja, Mercedes; Breit, Claudia; Clarke, Mitchell; Talar, Kamil; Wang, Kai; Mohammad, Mohammad A.; Pickwell, Sage; Etchandy, Guillermina; Stasiuk, Graeme J.; Sturge, Justin

2016-01-01

Here we describe a protocol that can be used to study the biophysical microenvironment related to increased thickness and stiffness of the basement membrane (BM) during age-related pathologies and metabolic disorders (e.g. cancer, diabetes, microvascular disease, retinopathy, nephropathy and neuropathy). The premise of the model is non-enzymatic crosslinking of reconstituted BM (rBM) matrix by treatment with glycolaldehyde (GLA) to promote advanced glycation endproduct (AGE) generation via the Maillard reaction. Examples of laboratory techniques that can be used to confirm AGE generation, non-enzymatic crosslinking and increased stiffness in GLA treated rBM are outlined. These include preparation of native rBM (treated with phosphate-buffered saline, PBS) and stiff rBM (treated with GLA) for determination of: its AGE content by photometric analysis and immunofluorescent microscopy, its non-enzymatic crosslinking by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) as well as confocal microscopy, and its increased stiffness using rheometry. The procedure described here can be used to increase the rigidity (elastic moduli, E) of rBM up to 3.2-fold, consistent with measurements made in healthy versus diseased human prostate tissue. To recreate the biophysical microenvironment associated with the aging and diseased prostate gland three prostate cell types were introduced on to native rBM and stiff rBM: RWPE-1, prostate epithelial cells (PECs) derived from a normal prostate gland; BPH-1, PECs derived from a prostate gland affected by benign prostatic hyperplasia (BPH); and PC3, metastatic cells derived from a secondary bone tumor originating from prostate cancer. Multiple parameters can be measured, including the size, shape and invasive characteristics of the 3D glandular acini formed by RWPE-1 and BPH-1 on native versus stiff rBM, and average cell length, migratory velocity and persistence of cell movement of 3D spheroids formed by PC3 cells under the same conditions. Cell signaling pathways and the subcellular localization of proteins can also be assessed. PMID:27684203

MAGIC-f Gel in Nuclear Medicine Dosimetry: study in an external beam of Iodine-131

NASA Astrophysics Data System (ADS)

Schwarcke, M.; Marques, T.; Garrido, C.; Nicolucci, P.; Baffa, O.

2010-11-01

MAGIC-f gel applicability in Nuclear Medicine dosimetry was investigated by exposure to a 131I source. Calibration was made to provide known absorbed doses in different positions around the source. The absorbed dose in gel was compared with a Monte Carlo Simulation using PENELOPE code and a thermoluminescent dosimetry (TLD). Using MRI analysis for the gel a R2-dose sensitivity of 0.23 s-1Gy-1was obtained. The agreement between dose-distance curves obtained with Monte Carlo simulation and TLD was better than 97% and for MAGIC-f and TLD was better than 98%. The results show the potential of polymer gel for application in nuclear medicine where three dimensional dose distribution is demanded.

Silicone gel breast implants: science and testing.

PubMed

Kinney, Brian M; Jeffers, Lynn L C; Ratliff, Gregory E; Carlisle, Dan A

2014-07-01

Since the first generation of breast implants, major design innovations, including consistency of the gel, palpability and thickness of the shell, and barrier materials in the shell, have been introduced. Surgeons have not had metrics to assess and compare available implants. Research at independent laboratories included 4 tests: gel elasticity (the gel's ability to retain its shape), gel compression fracture (the resistance to permanent gel deformation), gel-shell peel (the integration of the gel with shell as a cohesive unit), and morphological analysis. Sientra's round High-Strength Cohesive (HSC) experienced the least gel elasticity (5.805 mm), whereas Allergan's round implants experienced the most (7.465 mm). Among shaped implants, Allergan 410 experienced the least gel elasticity (3.242 mm), whereas the Sientra HSC+ implant experienced the most (4.270 mm). Sientra's round (36.32 lbf) and shaped (44.16 lbf) implants demonstrated the highest resistance to gel fracture, with Allergan's implants demonstrating the least among round (23.06 lbf) implants and Mentor Contour Profile Gel (CPG) among shaped (30.45 lbf) implants. For the gel-shell peel test, Sientra's implant required over 26% greater force than Allergan's implant and over 35% greater force than Mentor's implant. Sientra's shaped implants required more than double the peel force than Allergan 410 (119% greater) and Mentor CPG (130% greater). Morphological results showed Sientra's implants preserved structural integrity (-1.10% change). The initial findings show that these implant characteristics are individual factors to be considered separately and are not necessarily correlative. Further study of implants using these and other testing techniques will help clinicians choose between implants.

The effects of inhomogeneous boundary dilution on the coating flow of an anti-HIV microbicide vehicle

NASA Astrophysics Data System (ADS)

Tasoglu, Savas; Peters, Jennifer J.; Park, Su Chan; Verguet, Stéphane; Katz, David F.; Szeri, Andrew J.

2011-09-01

A recent study in South Africa has confirmed, for the first time, that a vaginal gel formulation of the antiretroviral drug Tenofovir, when topically applied, significantly inhibits sexual HIV transmission to women [Karim et al., Science 329, 1168 (2010)]. However, the gel for this drug and anti-HIV microbicide gels in general have not been designed using an understanding of how gel spreading and retention in the vagina govern successful drug delivery. Elastohydrodynamic lubrication theory can be applied to model spreading of microbicide gels [Szeri et al., Phys. Fluids 20, 083101 (2008)]. This should incorporate the full rheological behavior of a gel, including how rheological properties change due to contact with, and dilution by, ambient vaginal fluids. Here, we extend our initial analysis, incorporating the effects of gel dilution due to contact with vaginal fluid produced at the gel-tissue interface. Our original model is supplemented with a convective-diffusive transport equation to characterize water transport into the gel and, thus, local gel dilution. The problem is solved using a multi-step scheme in a moving domain. The association between local dilution of gel and rheological properties is obtained experimentally, delineating the way constitutive parameters of a shear-thinning gel are modified by dilution. Results show that dilution accelerates the coating flow by creating a slippery region near the vaginal wall akin to a dilution boundary layer, especially if the boundary flux exceeds a certain value. On the other hand, if the diffusion coefficient of boundary fluid is increased, the slippery region diminishes in extent and the overall rate of gel spreading decreases.

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

PubMed

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

1998-01-01

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

Physicochemical and immunologic characterization of low-molecular-weight allergoids of Dactylis glomerata pollen proteins.

PubMed

Cirković, T D; Bukilica, M N; Gavrović, M D; Vujcić, Z M; Petrović, S; Jankov, R M

1999-02-01

Orchard grass (Dactylis glomerata) pollen proteins were chemically modified by means of acid anhydrides (maleic and succinic anhydride) to obtain low-molecular-weight allergoids. Chemical modification in both cases led to the replacement of one positive charge (epsilon amino group of Lys) by one negative charge, yielding proteins with changed physicochemical properties in comparison to the native orchard grass-pollen proteins. Physicochemical characterization of derivatives was done by gel chromatography, SDS-PAGE, and isoelectric focusing. To examine the IgE-binding properties of these derivatives, we carried out immunoblotting. To examine the ability of derivatives to induce IgG production, we immunized rabbits. Skin prick testing with the allergoids was performed on 15 individuals allergic to orchard grass pollens and on two healthy subjects. It was shown that the modified proteins retain their original molecular weights, but change pI to more acidic values. In the case of allergoids, a strong reduction in IgE binding was found. Immunization of rabbits with allergoids showed that the derivatives retain the ability to induce IgG production, and that the antisera obtained in such a way react to native (unmodified) extract. The ability of derivatives to induce allergic reaction was significantly reduced. The patients (86.6%) included in our study exhibited less than 50% of native extract response. Among them, 53.3% had no response to one or both allergoids. These modification procedures yield allergoids with a reduced allergenic activity and preserved immunogenic potential suitable for use in immunotherapy.

Intensive management affects composition of betaproteobacterial ammonia oxidizers in turfgrass systems.

PubMed

Dell, Emily A; Bowman, Daniel; Rufty, Thomas; Shi, Wei

2008-07-01

Turfgrass is a highly managed ecosystem subject to frequent fertilization, mowing, irrigation, and application of pesticides. Turf management practices may create a perturbed environment for ammonia oxidizers, a key microbial group responsible for nitrification. To elucidate the long-term effects of turf management on these bacteria, we assessed the composition of betaproteobacterial ammonia oxidizers in a chronosequence of turfgrass systems (i.e., 1, 6, 23, and 95 years old) and the adjacent native pines by using both 16S rRNA and amoA gene fragments specific to ammonia oxidizers. Based on the Shannon-Wiener diversity index of denaturing gradient gel electrophoresis patterns and the rarefaction curves of amoA clones, turf management did not change the relative diversity and richness of ammonia oxidizers in turf soils as compared to native pine soils. Ammonia oxidizers in turfgrass systems comprised a suite of phylogenetic clusters common to other terrestrial ecosystems. Nitrosospira clusters 0, 2, 3, and 4; Nitrosospira sp. Nsp65-like sequences; and Nitrosomonas clusters 6 and 7 were detected in the turfgrass chronosequence with Nitrosospira clusters 3 and 4 being dominant. However, both turf age and land change (pine to turf) effected minor changes in ammonia oxidizer composition. Nitrosospira cluster 0 was observed only in older turfgrass systems (i.e., 23 and 95 years old); fine-scale differences within Nitrosospira cluster 3 were seen between native pines and turf. Further investigations are needed to elucidate the ecological implications of the compositional differences.

Synthesis and Fabrication of Collagen-Coated Ostholamide Electrospun Nanofiber Scaffold for Wound Healing.

PubMed

Kandhasamy, Subramani; Perumal, Sathiamurthi; Madhan, Balaraman; Umamaheswari, Narayanan; Banday, Javid Ahmad; Perumal, Paramasivan Thirumalai; Santhanakrishnan, Vichangal Pridiuldi

2017-03-15

A novel scaffold for effective wound healing treatment was developed utilizing natural product bearing collagen-based biocompatible electrospun nanofibers. Initially, ostholamide (OSA) was synthesized from osthole (a natural coumarin), characterized by 1 H, 13 C, DEPT-135 NMR, ESI-MS, and FT-IR spectroscopy analysis. OSA was incorporated into polyhydroxybutyrate (PHB) and gelatin (GEL), which serve as templates for electrospun nanofibers. The coating of OSA-PHB-GEL nanofibers with collagen resulted in PHB-GEL-OSA-COL nanofibrous scaffold which mimics extracellular matrix and serves as an effective biomaterial for tissue engineering applications, especially for wound healing. PHB-GEL-OSA-COL, along with PHB-GEL-OSA and collagen film (COLF), was characterized in vitro and in vivo to determine its efficacy. The developed PHB-GEL-OSA-COL nanofibers posed an impressive mechanical stability, an essential requirement for wound healing. The presence of OSA had contributed to antimicrobial efficacy. These scaffolds exhibited efficient antibacterial activity against common wound pathogens, Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus). The zones of inhibition were observed to be 14 ± 22 and 10 ± 2 mm, respectively. It was observed that nanofibrous scaffold had the ability to release OSA in a controlled manner, and hence, OSA would be present at the site of application and exhibit bioactivity in a sustained manner. PHB-GEL-OSA-COL nanofiber was determined to be stable against enzymatic degradation, which is the most important parameter for promoting proliferation of cells contributing to repair and remodeling of tissues during wound healing applications. As hypothesized, PHB-GEL-OSA-COL was observed to imbibe excellent cytocompatibility, which was determined using NIH 3T3 fibroblast cell proliferation studies. PHB-GEL-OSA-COL exhibited excellent wound healing efficacy which was confirmed using full thickness excision wound model in Wistar rats. The rats treated with PHB-GEL-OSA-COL nanofibrous scaffold displayed enhanced healing when compared to untreated control. Both in vitro and in vivo analysis of PHB-GEL-OSA-COL presents a strong case of therapeutic biomaterial suiting wound repair and regeneration.

3-(Triethoxysilyl)propionitrile sol-gel coating.

PubMed

Li, Ying-Sing; Xiao, Yun; Wright, Paul B; Tran, Tuan

2005-05-01

3-(Triethoxysilyl)propionitrile (TESPN) sol-gel has been prepared under different conditions. It was employed for coating the surfaces of quartz and aluminum. Infrared (IR) and Raman spectra of TESPN and TESPN sol-gels have been recorded in the study of the sol-gel process. Transmission and reflection absorption IR (RAIR) spectra of TESPN sol-gel coated quartz and aluminum have also been collected for better understanding the film formation on the substrate surfaces. Spectra collected at different temperatures indicated that the silane film on quartz decomposes at 700 degrees C. Results from thermal gravimetric analysis (TGA) supported this result. Based on the group frequencies and the spectral behavior in different states, some vibrational modes were assigned to the observed bands. The anticorrosion behavior of the sol-gel coated aluminum in comparison with the uncoated metal was evaluated by measuring the potentiodynamic polarization and electrochemical impedance spectra (EIS).

Examining the Heterogeneous Genome Content of Multipartite Viruses BMV and CCMV by Native Mass Spectrometry

NASA Astrophysics Data System (ADS)

van de Waterbeemd, Michiel; Snijder, Joost; Tsvetkova, Irina B.; Dragnea, Bogdan G.; Cornelissen, Jeroen J.; Heck, Albert J. R.

2016-06-01

Since the concept was first introduced by Brian Chait and co-workers in 1991, mass spectrometry of proteins and protein complexes under non-denaturing conditions (native MS) has strongly developed, through parallel advances in instrumentation, sample preparation, and data analysis tools. However, the success rate of native MS analysis, particularly in heterogeneous mega-Dalton (MDa) protein complexes, still strongly depends on careful instrument modification. Here, we further explore these boundaries in native mass spectrometry, analyzing two related endogenous multipartite viruses: the Brome Mosaic Virus (BMV) and the Cowpea Chlorotic Mottle Virus (CCMV). Both CCMV and BMV are approximately 4.6 megadalton (MDa) in mass, of which approximately 1 MDA originates from the genomic content of the virion. Both viruses are produced as mixtures of three particles carrying different segments of the genome, varying by approximately 0.1 MDA in mass (~2%). This mixture of particles poses a challenging analytical problem for high-resolution native MS analysis, given the large mass scales involved. We attempt to unravel the particle heterogeneity using both Q-TOF and Orbitrap mass spectrometers extensively modified for analysis of very large assemblies. We show that manipulation of the charging behavior can provide assistance in assigning the correct charge states. Despite their challenging size and heterogeneity, we obtained native mass spectra with resolved series of charge states for both BMV and CCMV, demonstrating that native MS of endogenous multipartite virions is feasible.

A rapid high-resolution method for resolving DNA topoisomers.

PubMed

Mitchenall, Lesley A; Hipkin, Rachel E; Piperakis, Michael M; Burton, Nicolas P; Maxwell, Anthony

2018-01-16

Agarose gel electrophoresis has been the mainstay technique for the analysis of DNA samples of moderate size. In addition to separating linear DNA molecules, it can also resolve different topological forms of plasmid DNAs, an application useful for the analysis of the reactions of DNA topoisomerases. However, gel electrophoresis is an intrinsically low-throughput technique and suffers from other potential disadvantages. We describe the application of the QIAxcel Advanced System, a high-throughput capillary electrophoresis system, to separate DNA topoisomers, and compare this technique with gel electrophoresis. We prepared a range of topoisomers of plasmids pBR322 and pUC19, and a 339 bp DNA minicircle, and compared their separation by gel electrophoresis and the QIAxcel System. We found superior resolution with the QIAxcel System, and that quantitative analysis of topoisomer distributions was straightforward. We show that the QIAxcel system has advantages in terms of speed, resolution and cost, and can be applied to DNA circles of various sizes. It can readily be adapted for use in compound screening against topoisomerase targets.

Synthesis of hybrid cellulose nanocomposite bonded with dopamine SiO2/TiO2 and its antimicrobial activity

NASA Astrophysics Data System (ADS)

Ramesh, Sivalingam; Kim, Gwang-Hoon; Kim, Jaehwan; Kim, Joo-Hyung

2015-04-01

Organic-inorganic hybrid material based cellulose was synthesized by the sol-gel approach. The explosion of activity in this area in the past decade has made tremendous progress in industry or academic both fundamental understanding of sol-gel process and applications of new functionalized hybrid materials. In this present research work, we focused on cellulose-dopamine functionalized SiO2/TiO2 hybrid nanocomposite by sol-gel process. The cellulose-dopamine hybrid nanocomposite was synthesized via γ-aminopropyltriethoxysilane (γ-APTES) coupling agent by in-situ sol-gel process. The chemical structure of cellulose-amine functionalized dopamine bonding to cellulose structure with covalent cross linking hybrids was confirmed by FTIR spectral analysis. The morphological analysis of cellulose-dopamine nanoSiO2/TiO2 hybrid nanocomposite materials was characterized by XRD, SEM and TEM. From this different analysis results indicate that the optical transparency, thermal stability, control morphology of cellulose-dopamine-SiO2/TiO2 hybrid nanocomposite. Furthermore cellulose-dopamine-SiO2/TiO2 hybrid nanocomposite was tested against pathogenic bacteria for antimicrobial activity.

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

PubMed

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

2013-02-01

The ability of food gels to hold water affects product yield and organoleptic quality. Most researchers believe that water is held by capillarity such that gels having smaller mean pore diameter and a more hydrophilic surface hold water more tightly. To date, however, only qualitative evidence relating pore size to water holding (WH) properties has been provided. The present study sought to provide quantitative confirmation of this hypothesis. Scanning electron microscopy coupled with image analysis was used to measure pore size, and water contact angle with the gel surface was measured by the captive bubble method, in both model polyacrylamide gels and heat-induced protein (minced chicken breast) gels. These were related to water lost during cooking of meat pastes to form gels (cooking loss (CL)), as well as water lost upon centrifugation (expressible water (EW)) or by capillary suction (CSL) of all prepared gels, as inverse measures of WH. As predicted by the Young-Laplace equation for calculating capillary pressure, the presumed mechanism of WH, gels with lower water losses exhibited a more hydrophilic surface (smaller contact angle). Yet, both lower CL and CSL correlated with larger mean pore diameter of gels, not smaller as had been expected. Polyacrylamide gels varied more in WH than did prepared meat gels, yet only the capillary suction method was sensitive enough to detect these differences.  The ability of gels to hold water is important for economics of processing, food quality, and food safety. This study investigated the prevailing theory for how gels hold water, capillarity. Both the pore sizes of gel microstructures and the degree of hydrophilicity of the polymers comprising each gel were quantitatively assessed and related to water holding (WH) properties, and this was the first report using such methodologies. It appeared that the degree of hydrophilicity was much more important explaining WH properties than pore size, and that future research of this kind should be carried out. © 2013 Institute of Food Technologists®

Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

NASA Astrophysics Data System (ADS)

Belov, Arseniy M.; Viner, Rosa; Santos, Marcia R.; Horn, David M.; Bern, Marshall; Karger, Barry L.; Ivanov, Alexander R.

2017-12-01

Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). [Figure not available: see fulltext.

Purification and Characterization of a Novel Thermostable α-l-Arabinofuranosidase from a Color-Variant Strain of Aureobasidium pullulans

PubMed Central

Saha, Badal C.; Bothast, Rodney J.

1998-01-01

A color-variant strain of Aureobasidium pullulans (NRRL Y-12974) produced α-l-arabinofuranosidase (α-l-AFase) when grown in liquid culture on oat spelt xylan. An extracellular α-l-AFase was purified 215-fold to homogeneity from the culture supernatant by ammonium sulfate treatment, DEAE Bio-Gel A agarose column chromatography, gel filtration on a Bio-Gel A-0.5m column, arabinan-Sepharose 6B affinity chromatography, and SP-Sephadex C-50 column chromatography. The purified enzyme had a native molecular weight of 210,000 and was composed of two equal subunits. It had a half-life of 8 h at 75°C, displayed optimal activity at 75°C and pH 4.0 to 4.5, and had a specific activity of 21.48 μmol · min−1 · mg−1 of protein against p-nitrophenyl-α-l-arabinofuranoside (pNPαAF). The purified α-l-AFase readily hydrolyzed arabinan and debranched arabinan and released arabinose from arabinoxylans but was inactive against arabinogalactan. The Km values of the enzyme for the hydrolysis of pNPαAF, arabinan, and debranched arabinan at 75°C and pH 4.5 were 0.26 mM, 2.14 mg/ml, and 3.25 mg/ml, respectively. The α-l-AFase activity was not inhibited at all by l-arabinose (1.2 M). The enzyme did not require a metal ion for activity, and its activity was not affected by p-chloromercuribenzoate (0.2 mM), EDTA (10 mM), or dithiothreitol (10 mM). PMID:9435077

Radioiodination of scorpion and snake toxins. [/sup 125/I, /sup 127/I

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

Rochat, H.; Tessier, M.; Miranda, F.

1977-10-01

Several scorpion and snake toxins were radioiodinated using the lactoperoxydase method of (/sup 125/I)iodide oxidation. Two techniques of labeling were set up: Using carrier-free Na/sup 125/I and 5 ..mu..g of toxin, about one iodine atom was incorporated per mole of protein without loss of toxicity. Specific radioactivities about 2,000 Ci/mmol (280 ..mu..Ci/..mu..g) were obtained. The modified toxin, purified by immunoprecipitation with an antiserum prepared against the native toxin, was obtained in a short time (4 hr), with a good yield (50 to 80%), and in a small volume (1 ml). Using Na/sup 127/I traced with Na /sup 125/I and largermore » amounts (200 ..mu..g) of toxin, more than one iodine atom was incorporated per mole of protein without loss of activity. Lower specific radioactivities (1 to 1.5 Ci/mmol) were obtained. The iodinated toxins were purified by gel filtration of the radioiodination mixtures on a column made of two layers of Sephadex (G-15 and G-50). The modified proteins were extensively analyzed by paper electrophoresis and polyacrylamide gel electrophoresis. Their content of monoiodotyrosine and diiodotyrosine was estimated and, in the case of toxin I of Androctonus australis Hector, it was possible to follow the iodination rate of its three tyrosine residues by automatic Edman degradation. The mode of purification of the iodinated scorpion toxins affects their behavior on molecular sieving on Sephadex G-50 and on electrophoresis on polyacrylamide gel. The results are discussed.« less

Purification and characterization of an alkaline protease Prot 1 from Botrytis cinerea : biodetergent catalyst assay.

PubMed

Abidi, Ferid; Limam, Ferid; Marzouki, M Nejib

2007-01-01

Alkaline thiol protease named Prot 1 was isolated from a culture filtrate of Botrytis cinerea. The enzyme was purified by ammonium sulfate fractionation, gel filtration, and ion-exchange chromatography. Thus, the enzyme was purified to homogeneity with specific activity of 30-fold higher than that of the crude broth. The purified alkaline protease has an apparent molecular mass of 43 kDa under denaturing conditions as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The native molecular mass (45 kDa), determined by gel filtration, indicated that the alkaline protease has a monomeric form. The purified protease was biochemically characterized. The enzyme is active at alkaline pH and has a suitable and high thermostability. The optimal pH and temperature for activity were 9.0-10.0 and 60 degrees C, respectively. This protease was stable between pH 5.0 and 12.0. The enzyme retained 85% of its activity by treatment at 50 degrees C over 120 min; it maintained 50% of activity after 60 min of heating at 60 degrees C. Furthermore, the protease retained almost complete activity after 4 wk storage at 25 degrees C. The activity was significantly affected by thiol protease inhibitors, suggesting that the enzyme belongs to the alkaline thiol protease family. With the aim on industrial applications, we focused on studying the stability of the protease in several conditions. Prot 1 activity was not affected by ionic strength and different detergent additives, and, thus, the protease shows remarkable properties as a biodetergent catalyst.

Purification and characterization of akr1b10 from human liver: role in carbonyl reduction of xenobiotics.

PubMed

Martin, Hans-Jörg; Breyer-Pfaff, Ursula; Wsol, Vladimir; Venz, Simone; Block, Simone; Maser, Edmund

2006-03-01

Members of the aldo-keto reductase (AKR) superfamily have a broad substrate specificity in catalyzing the reduction of carbonyl group-containing xenobiotics. In the present investigation, a member of the aldose reductase subfamily, AKR1B10, was purified from human liver cytosol. This is the first time AKR1B10 has been purified in its native form. AKR1B10 showed a molecular mass of 35 kDa upon gel filtration and SDS-polyacrylamide gel electrophoresis. Kinetic parameters for the NADPH-dependent reduction of the antiemetic 5-HT3 receptor antagonist dolasetron, the antitumor drugs daunorubicin and oracin, and the carcinogen 4-methylnitrosamino-1-(3-pyridyl)-1-butanone (NNK) to the corresponding alcohols have been determined by HPLC. Km values ranged between 0.06 mM for dolasetron and 1.1 mM for daunorubicin. Enzymatic efficiencies calculated as kcat/Km were more than 100 mM-1 min-1 for dolasetron and 1.3, 0.43, and 0.47 mM-1 min-1 for daunorubicin, oracin, and NNK, respectively. Thus, AKR1B10 is one of the most significant reductases in the activation of dolasetron. In addition to its reducing activity, AKR1B10 catalyzed the NADP+-dependent oxidation of the secondary alcohol (S)-1-indanol to 1-indanone with high enzymatic efficiency (kcat/Km=112 mM-1 min-1). The gene encoding AKR1B10 was cloned from a human liver cDNA library and the recombinant enzyme was purified. Kinetic studies revealed lower activity of the recombinant compared with the native form. Immunoblot studies indicated large interindividual variations in the expression of AKR1B10 in human liver. Since carbonyl reduction of xenobiotics often leads to their inactivation, AKR1B10 may play a role in the occurrence of chemoresistance of tumors toward carbonyl group-bearing cytostatic drugs.

INVESTIGATION OF DNA REPAIR BY SISTER CHROMATID EXCHANGE (SCE) ANALYSIS AND THE ALKALINE SINGLE CELL GEL ASSAY (SCG) IN MAMMALIAN GO-LYMPHOCYTES AFTER IN VITRO EXPOSURE TO ETHYLENE OXIDE (EO)

EPA Science Inventory

Investigation ofDNA Repair by Sister Chromatid Exchange (SCE) Analysis and the Alkaline Single Cell Gel Assay (SCG) in Mammalian Go-Lymphocytes after In Vitro Exposure to Ethylene Oxide (EO).

EO is a large volume chemical used primarily as an intermediate in manufacturing...

Effect of natural gel product on bovine dentin erosion in vitro

PubMed Central

SALES-PERES, André de Carvalho; MARSICANO, Juliane Avansini; GARCIA, Rudan Paraíso; FORIM, Moacir Rossi; da SILVA, Maria Fatima das Graças Fernandes; SALES-PERES, Sílvia Helena de Carvalho

2013-01-01

Objective To evaluate the efficacy of Neem (Azadirachta indica) experimental gel for the prevention of erosive wear on bovine dentin, in vitro. Material and Methods One hundred dentin blocks were allocated into 5 experimental groups (20 samples each): C (control group, without gel); CG (control group, only base gel); F (fluoride gel, 1.23% NaF; pH 4.1, Dentsply; Brazil); N (Neem gel, 10% neem extract; pH 4.1, manipulation); NF (Neem+fluoride gel, 10% Neem extract and 1.23% NaF; pH 4.1, manipulation). The blocks were stored in artificial saliva for 24 hours. After this, they were submitted to six alternating re- and demineralization cycles. The blocks were analyzed for wear (profilometry). The results were submitted to statistical analysis by ANOVA and Tukey tests (P<0.05). Results The mean wear (±SD, µm) was shown as follows in groups: C (13.09±0.99), CG (10.60±1.99), F (10.90±1.44), N (12.68±1.13) and NF (10.84±1.65). All gels showed some preventive action when compared with control group. However, significant differences were found only between Neem+fluoride gel and fluoride gel. Conclusion A single application of a neem-containing fluoride gel reduced dentin erosion, thus it is a possible alternative in reducing dental wear. Further research should investigate the action mechanism and the synergism between them. PMID:24473728

Parameterization of the InVEST Crop Pollination Model to spatially predict abundance of wild blueberry (Vaccinium angustifolium Aiton) native bee pollinators in Maine, USA

USGS Publications Warehouse

Groff, Shannon C.; Loftin, Cynthia S.; Drummond, Frank; Bushmann, Sara; McGill, Brian J.

2016-01-01

Non-native honeybees historically have been managed for crop pollination, however, recent population declines draw attention to pollination services provided by native bees. We applied the InVEST Crop Pollination model, developed to predict native bee abundance from habitat resources, in Maine's wild blueberry crop landscape. We evaluated model performance with parameters informed by four approaches: 1) expert opinion; 2) sensitivity analysis; 3) sensitivity analysis informed model optimization; and, 4) simulated annealing (uninformed) model optimization. Uninformed optimization improved model performance by 29% compared to expert opinion-informed model, while sensitivity-analysis informed optimization improved model performance by 54%. This suggests that expert opinion may not result in the best parameter values for the InVEST model. The proportion of deciduous/mixed forest within 2000 m of a blueberry field also reliably predicted native bee abundance in blueberry fields, however, the InVEST model provides an efficient tool to estimate bee abundance beyond the field perimeter.

Gluten gel and film properties in the presence of cysteine and sodium alginate.

PubMed

Yuno-Ohta, Naoko; Yamada, Mariko; Inomata, Masako; Konagai, Hiromi; Kataoka, Tomomi

2009-08-01

Wheat flour has an ability of forming dough by mixing with water, which exhibits a rheological property required for making bread. The major protein is gluten, which is a valuable protein material for food industry. In this study, gluten protein gels and films were formed with cysteine and sodium alginate. Adding cysteine improved gel and film properties (stress relaxation behavior, bending strength). The gel containing 0.01 M cysteine had a longer relaxation time and was more rigid than the gel without cysteine. Although adding sodium alginate to the gluten suspension containing cysteine improved the water-holding ability and homogeneity of the gel network, the film from this gel was more brittle than the gluten film with cysteine alone. Microstructural observations of the gels and films with scanning electron microscopy suggested that water evaporation was more heterogeneous from the gel containing sodium alginate than from the gel with cysteine alone. Fourier transform-infrared (FT-IR) analysis during film formation suggested that the presence of cysteine encourages interaction between gluten molecules and results in intermolecular beta-sheet formation in earlier stages than in the no additive condition. FT-IR results also suggested that the combined effect of sodium alginate and cysteine on the protein secondary structure was remarkably different from that of cysteine alone. Our results suggest that addition of a suitable amount of cysteine (0.01 M) and heat treatment to 80 degrees C during gluten gel and film formation induces a homogenous network in the gel and film by regulating disulfide-sulfide interactions.

Electromyography analysis of natural mastication behavior using varying mouthful quantities of two types of gels.

PubMed

Kohyama, Kaoru; Gao, Zhihong; Ishihara, Sayaka; Funami, Takahiro; Nishinari, Katsuyoshi

2016-07-01

The objectives of this study were to examine the effects of mouthful quantities and mechanical properties of gels on natural mastication behaviors using electromyography (EMG). Two types of hydrocolloid gels (A and K) with similar fracture loads but different moduli and fracture strains were served to eleven normal women in 3-, 6-, 12-, and 24-g masses in a randomized order. EMG activities from both masseter muscles were recorded during natural mastication. Because of the similar fracture loads, the numbers of chews, total muscle activities, and entire oral processing times were similar for similar masses of both gel types. Prior to the first swallow, the more elastic K gel with a higher fracture strain required higher muscle activities than the brittle A gel, which had higher modulus. Majority of subjects had preferred sides of chewing, but all subjects with or without preferred sides used both masseters during the consumption of gels. Similar effects of masses and types of gels were observed in EMG activities of both sides of masseters. Contributions of the dominant side of chewing were diminished with increasing masses of gels, and the mass dependency on ratio of the dominant side was more pronounced with K gel. More repetitions of smaller masses required greater muscle activities and longer periods for the consumption of 24-g gel portions. Reduction in the masses with an increased number of repetitions necessitated slower eating and more mastication to consume the gel portions. These observations suggest that chewing using both sides is more effective and unconsciously reduces mastication times during the consumption of gels. Copyright © 2016 Elsevier Inc. All rights reserved.

The characterization of hydroxypropyl methylcellulose through the analysis of its substituents

USDA-ARS?s Scientific Manuscript database

The methyl and hydroxypropyl substituents in hydroxypropyl methylcellulose (HPMC) affect the resulting gel properties. These substituents in five HPMC gels were characterized using Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, small-amplitude oscillatory shear measurements, a...

Effects of heating and calcium and phosphate mineral supplementation on the physical properties of rennet-induced coagulation of camel and cow milk gels.

PubMed

Kamal, Mohammad; Foukani, Mohammed; Karoui, Romdhane

2017-05-01

The physical properties of rennet-induced coagulation of preheated camel and cow milk gels (50 and 70 °C for 10 min) enriched with calcium chloride (CaCl2) and hydrogen phosphate dihydrate (Na2HPO42H2O) were evaluated using the dynamic low amplitude oscillatory shear analysis. The storage modulus (G') and loss modulus (G") of camel milk gels showed significant (P < 0·05) lower values than those of cow milk gels. The preheating of camel milk at 50 °C affected negatively the gelation properties, while the preheating at 70 °C prevented the formation of rennet-induced milk gels. No effect was observed on the gelation properties of cow milk gels. The CaCl2 added at 10 and 20 mM to preheated camel and cow milk reduced significantly (P < 0·05) the gelation time and increased the gel firmness. In contrast, Na2HPO42H2O added at 10 and 20 mM induced the formation of weak gels for preheated camel and cow milk at 50 °C, and even no gelation for preheated camel milk at 70 °C.

Cholesterol biosensor based on a plastic optical fibre with sol-gel: structural analysis and sensing properties

NASA Astrophysics Data System (ADS)

Razo-Medina, D. A.; Trejo-Durán, M.; Alvarado-Méndez, E.

2018-02-01

In this paper, we report the design and characterization of an optical fibre cholesterol biosensor by using sol-gel immobilization technique. The cholesterol enzyme is encapsulated inside of the sol-gel film onto an end of a plastic optical fibre. Two film deposition methods (Dip-Coating and Immersion) were studied. The morphology analysis and sensing properties permit us to determine the best film deposition to sense cholesterol concentration. The range of measured is 4.4-5.2 mM in real time and our results were validated by comparing them with other previously published results. The biosensor is portable, simple cheap, and easy to use.

Urea functionalized surface-bonded sol-gel coating for on-line hyphenation of capillary microextraction with high-performance liquid chromatography.

PubMed

Jillani, Shehzada Muhammad Sajid; Alhooshani, Khalid

2018-03-30

Sol-gel urea functionalized-[bis(hydroxyethyl)amine] terminated polydimethylsiloxane coating was developed for capillary microextraction-high performance liquid chromatographic analysis from aqueous samples. A fused silica capillary is coated from the inside with surface bonded coating material and is created through in-situ sol-gel reaction. The urea-functionalized coating was immobilized to the inner surface of the capillary by the condensation reaction of silanol groups of capillary and sol-solution. The characterization of the coating material was successfully done by using X-ray photoelectron spectroscopy, thermogravimetric analysis, field emission scanning electron microscope, and energy dispersive X-ray spectrometer. To make a setup of online capillary microextraction-high performance liquid chromatography, the urea functionalized capillary was installed in the HPLC manual injection port. The analytes of interest were pre-concentrated in the coated sampling loop, desorbed by the mobile phase, chromatographically separated on C-18 column, and analyzed by UV detector. Sol-gel coated capillaries were used for online extraction and high-performance liquid chromatographic analysis of phenols, ketones, aldehydes, and polyaromatic hydrocarbons. This newly developed coating showed excellent extraction for a variety of analytes ranging from highly polar to non-polar in nature. The analysis using sol-gel coating showed excellent overall sensitivity in terms of lower detection limits (S/N = 3) for the analytes (0.10 ng mL -1 -14.29 ng mL -1 ) with acceptable reproducibility that is less than 12.0%RSD (n = 3). Moreover, the capillary to capillary reproducibility of the analysis was also tested by changing the capillary of the same size. This provided excellent%RSD of less than 10.0% (n = 3). Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Graphical analysis for gel morphology II. New mathematical approach for stretched exponential function with β>1

NASA Astrophysics Data System (ADS)

Hashimoto, Chihiro; Panizza, Pascal; Rouch, Jacques; Ushiki, Hideharu

2005-10-01

A new analytical concept is applied to the kinetics of the shrinking process of poly(N-isopropylacrylamide) (PNIPA) gels. When PNIPA gels are put into hot water above the critical temperature, two-step shrinking is observed and the secondary shrinking of gels is fitted well by a stretched exponential function. The exponent β characterizing the stretched exponential is always higher than one, although there are few analytical concepts for the stretched exponential function with β>1. As a new interpretation for this function, we propose a superposition of step (Heaviside) function and a new distribution function of characteristic time is deduced.

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.

Engineering a collagen matrix that replicates the biological properties of native extracellular matrix.

PubMed

Nam, Kwangwoo; Sakai, Yuuki; Funamoto, Seiichi; Kimura, Tsuyoshi; Kishida, Akio

2011-01-01

In this study, we aimed to replicate the function of native tissues that can be used in tissue engineering and regenerative medicine. The key to such replication is the preparation of an artificial collagen matrix that possesses a structure resembling that of the extracellular matrix. We, therefore, prepared a collagen matrix by fibrillogenesis in a NaCl/Na(2)HPO(4) aqueous solution using a dialysis cassette and investigated its biological behavior in vitro and in vivo. The in vitro cell adhesion and proliferation did not show any significant differences. The degradation rate in the living body could be controlled according to the preparation condition, where the collagen matrix with high water content (F-collagen matrix, >98%) showed fast degradation and collagen matrix with lower water content (T-collagen matrix, >80%) showed no degradation for 8 weeks. The degradation did not affect the inflammatory response at all and relatively faster wound healing response was observed. Comparing this result with that of collagen gel and decellularized cornea, it can be concluded that the structural factor is very important and no cell abnormal behavior would be observed for quaternary structured collagen matrix.

Using an FPLC to promote active learning of the principles of protein structure and purification.

PubMed

Robinson, Rebekah L; Neely, Amy E; Mojadedi, Wais; Threatt, Katie N; Davis, Nicole Y; Weiland, Mitch H

2017-01-02

The concepts of protein purification are often taught in undergraduate biology and biochemistry lectures and reinforced during laboratory exercises; however, very few reported activities allow students to directly gain experience using modern protein purification instruments, such as Fast Protein Liquid Chromatography (FPLC). This laboratory exercise uses size exclusion chromatography (SEC) and ion exchange (IEX) chromatography to separate a mixture of four different proteins. Students use an SEC chromatogram and corresponding SDS-PAGE gel to understand how protein conformations change under different conditions (i.e. native and non-native). Students explore strategies to separate co-eluting proteins by IEX chromatography. Using either cation or anion exchange, one protein is bound to the column while the other is collected in the flow-through. In this exercise, undergraduate students gain hands-on experience with experimental design, buffer and sample preparation, and implementation of instrumentation that is commonly used by experienced researchers while learning and applying the fundamental concepts of protein structure, protein purification, and SDS-PAGE. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):60-68, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

Rhizomucor miehei triglyceride lipase is processed and secreted from transformed Aspergillus oryzae.

PubMed

Huge-Jensen, B; Andreasen, F; Christensen, T; Christensen, M; Thim, L; Boel, E

1989-09-01

The cDNA encoding the precursor of the Rhizomucor miehei triglyceride lipase was inserted in an Aspergillus oryzae expression vector. In this vector the expression of the lipase cDNA is under control of the Aspergillus oryzae alpha-amylase gene promoter and the Aspergillus niger glucoamylase gene terminator. The recombinant plasmid was introduced into Aspergillus oryzae, and transformed colonies were selected and screened for lipase expression. Lipase-positive transformants were grown in a small fermentor, and recombinant triglyceride lipase was purified from the culture broth. The purified enzymatically active recombinant lipase (rRML) secreted from A. oryzae was shown to have the same characteristics with respect to mobility on reducing SDS-gels and amino acid composition as the native enzyme. N-terminal amino acid sequencing indicated that approximately 70% of the secreted rRML had the same N-terminal sequence as the native Rhizomucor miehei enzyme, whereas 30% of the secreted rRML was one amino acid residue shorter in the N-terminal. The recombinant lipase precursor, which has a 70 amino acid propeptide, is thus processed in and secreted from Aspergillus oryzae. We have hereby demonstrated the utility of this organism as a host for the production of recombinant triglyceride lipases.

Refolding and purification of recombinant L-asparaginase from inclusion bodies of E. coli into active tetrameric protein

PubMed Central

Upadhyay, Arun K.; Singh, Anupam; Mukherjee, K. J.; Panda, Amulya K.

2014-01-01

A tetrameric protein of therapeutic importance, Escherichia coli L-asparaginase-II was expressed in Escherichia coli as inclusion bodies (IBs). Asparaginase IBs were solubilized using low concentration of urea and refolded into active tetrameric protein using pulsatile dilution method. Refolded asparaginase was purified in two steps by ion-exchange and gel filtration chromatographic techniques. The recovery of bioactive asparaginase from IBs was around 50%. The melting temperature (Tm) of the purified asparaginase was found to be 64°C. The specific activity of refolded, purified asparaginase was found to be comparable to the commercial asparaginase (190 IU/mg). Enzymatic activity of the refolded asparaginase was high even at four molar urea solutions, where the IB aggregates are completely solubilized. From the comparison of chemical denaturation data and activity at different concentrations of guanidine hydrochloride, it was observed that dissociation of monomeric units precedes the complete loss of helical secondary structures. Protection of the existing native-like protein structure during solubilization of IB aggregates with 4 M urea improved the propensity of monomer units to form oligomeric structure. Our mild solubilization technique retaining native-like structures, improved recovery of asparaginase in bioactive tetrameric form. PMID:25309524

Laser Desorption Mass Spectrometry for DNA Sequencing and Analysis

NASA Astrophysics Data System (ADS)

Chen, C. H. Winston; Taranenko, N. I.; Golovlev, V. V.; Isola, N. R.; Allman, S. L.

1998-03-01

Rapid DNA sequencing and/or analysis is critically important for biomedical research. In the past, gel electrophoresis has been the primary tool to achieve DNA analysis and sequencing. However, gel electrophoresis is a time-consuming and labor-extensive process. Recently, we have developed and used laser desorption mass spectrometry (LDMS) to achieve sequencing of ss-DNA longer than 100 nucleotides. With LDMS, we succeeded in sequencing DNA in seconds instead of hours or days required by gel electrophoresis. In addition to sequencing, we also applied LDMS for the detection of DNA probes for hybridization LDMS was also used to detect short tandem repeats for forensic applications. Clinical applications for disease diagnosis such as cystic fibrosis caused by base deletion and point mutation have also been demonstrated. Experimental details will be presented in the meeting. abstract.

Sol-gel niobia sorbent with a positively charged octadecyl ligand providing enhanced enrichment of nucleotides and organophosphorus pesticides in capillary microextraction for online HPLC analysis.

PubMed

Kesani, Sheshanka; Malik, Abdul

2018-04-01

A niobia-based sol-gel organic-inorganic hybrid sorbent carrying a positively charged C 18 ligand (Nb 2 O 5 -C 18 (+ve)) was synthesized to achieve enhanced enrichment capability in capillary microextraction of organophosphorus compounds (which include organophosphorus pesticides and nucleotides) before their online analysis by high-performance liquid chromatography. The sorbent was designed to simultaneously provide three different types of molecular level interactions: electrostatic, Lewis acid-base, and van der Waals interactions. To understand relative contributions of various molecular level analyte-sorbent interactions in the extraction process, two other sol-gel niobia sorbents were also created: (a) a purely inorganic sol-gel niobia sorbent (Nb 2 O 5 ) and (b) an organic-inorganic hybrid sol-gel niobia sorbent carrying an electrically neutral-bonded octadecyl ligand (Nb 2 O 5 -C 18 ). The extraction efficiency of the created sol-gel niobia sorbent (Nb 2 O 5 -C 18 (+ve)) was compared with that of analogously designed and synthesized titania-based sol-gel sorbent (TiO 2 -C 18 (+ve)), taking into consideration that titania-based sorbents present state-of-the-art extraction media for organophosphorus compounds. In capillary microextraction with high-performance liquid chromatography analysis, Nb 2 O 5 -C 18 (+ve) had shown 40-50% higher specific extraction values (a measure of extraction efficiency) over that of TiO 2 -C 18 (+ve). Compared to TiO 2 -C 18 (+ve), Nb 2 O 5 -C 18 (+ve) also provided superior analyte desorption efficiency (96 vs. 90%) during the online release of the extracted organophosphorus pesticides from the sorbent coating in the capillary microextraction capillary to the chromatographic column using reversed-phase high-performance liquid chromatography mobile phase. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The effect of the methanol extract of Galium mite on the cellular immunity and antibody synthesis.

PubMed

Amirghofran, Zahra; Javidnia, Katayoun; Bahmani, Masood; Azadmehr, Abbas; Esmaeilbeig, Maryam

2011-01-01

In the present study, the immunomodulatory effects of Galium mite, a native herb used for the treatment of inflammation in Iranian traditional medicine, was investigated. The methanolic extract of the plant was prepared and examined for in vivo cell-mediated and humoral immunity against antigen in mice. Galium mite stimulated delayed type hypersensitivity at lower concentrations and inhibited the reaction at higher ones (p < 0.05). A dose-related decrease in primary and secondary antibody titer was observed in mice treated with the extract (p < 0.006). The extract at higher concentrations significantly reduced the proliferation of human-activated lymphocytes (p < 0.001). Cell cycle analysis on human lymphocytes treated with the extract showed an increase in the number of cells in sub-G1 region, indicating the ability of the extract to induce apoptosis in these cells. Induction of apoptosis was confirmed by DNA laddering on gel electrophoresis. In conclusion, G. mite has the ability to modulate cellular and humoral immune responses to the antigenic challenge and affect the rate of cell proliferation due to induction of apoptosis in the lymphocytes.

Separating esterase targets of organophosphorus compounds in the brain by preparative chromatography.

PubMed

Mangas, I; Vilanova, E; Benabent, M; Estévez, J

2014-02-10

Low level exposure to organophosphorus esters (OPs) may cause long-term neurological effects and affect specific cognition domains in experimental animals and humans. Action on known targets cannot explain most of these effects by. Soluble carboxylesterases (EC 3.1.1.1) of chicken brain have been kinetically discriminated using paraoxon, mipafox and phenylmethyl sulfonylfluoride as inhibitors and phenyl valerate as a substrate. Three different enzymatic components were discriminated and called Eα, Eβ and Eγ. In this work, a fractionation procedure with various steps was developed using protein native separation methods by preparative HPLC. Gel permeation chromatography followed by ion exchange chromatography allowed enriched fractions with different kinetic behaviors. The soluble chicken brain fraction was fractionated, while total esterase activity, proteins and enzymatic components Eα, Eβ and Eγ were monitored in each subfraction. After the analysis, 13 fractions were pooled and conserved. Preincubation of the soluble chicken brain fraction of with the organophosphorus mipafox gave rise to a major change in the ion exchange chromatography profile, but not in the molecular exchanged chromatography profile, which suggest that mipafox permanently modifies the ionic properties of numerous proteins. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Changes in bacterial community after application of three different herbicides.

PubMed

Moretto, Jéssica Aparecida Silva; Altarugio, Lucas Miguel; Andrade, Pedro Avelino; Fachin, Ana Lúcia; Andreote, Fernando Dini; Stehling, Eliana Guedes

2017-07-06

The native soil microbiota is very important to maintain the quality of that environment, but with the intensive use of agrochemicals, changes in microbial biomass and formation of large quantities of toxic waste were observed in soil, groundwater and surface water. Thereby, the goal of this study was to evaluate if the selective pressure exerted by the presence of the herbicides atrazine, diuron and 2,4-D changes the bacterial community structure of an agricultural soil, using denaturing gradient gel electrophoresis technique. According to PERMANOVA analysis, a greater effect of the herbicide persistence time in the soil, the effect of the herbicide class and the effect of interaction between these two factors (persistence time and herbicide class) were observed. In conclusion, the results showed that the selective pressure exerted by the presence of these herbicides altered the composition of the local microbiota, being atrazine and diuron that most significantly affected the bacterial community in soil, and the herbicide 2,4-D was the one that less altered the microbial community and that bacterial community was reestablished first. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

PCR synthesis of double stranded DNA labeled with 5-bromouridine. A step towards finding a bromonucleoside for clinical trials.

PubMed

Michalska, Barbara; Sobolewski, Ireneusz; Polska, Katarzyna; Zielonka, Justyna; Zylicz-Stachula, Agnieszka; Skowron, Piotr; Rak, Janusz

2011-12-05

Incorporation of 5-bromouridine (5BrdU) into DNA makes it sensitive to UV and ionizing radiation, which opens up a prospective route for the clinical usage of 5-bromouridine and other halonucleosides. In the present work the polymerase chain reaction (PCR) protocol, which enables a long DNA fragment (resembling DNA synthesized in the cell in the presence of halonucleosides) to be completely substituted with 5BrdU, was optimized. Using HPLC coupled to enzymatic digestion, it was demonstrated that the actual amounts of native nucleosides and 5BrdU correspond very well to those calculated from the sequence of PCR products. The synthesized DNA is photosensitive to photons of 300nm. HPLC analysis demonstrated that the photolysis of labeled PCR products leads to a significant decrease in the 5BrdU signal and the simultaneous occurrence of a uridine peak. Agarose and polyacrylamide gel electrophoresis suggest that single strand breaks and cross-links are formed as a result of UV irradiation. The PCR protocol described in the current paper may be employed for labeling DNA not only with BrdU but also with other halonucleosides. Copyright © 2011 Elsevier B.V. All rights reserved.

Outer Membrane Vesicles Derived from Salmonella Enteritidis Protect against the Virulent Wild-Type Strain Infection in a Mouse Model.

PubMed

Liu, Qiong; Yi, Jie; Liang, Kang; Zhang, Xiangmin; Liu, Qing

2017-08-28

Foodborne contamination and salmonellosis caused by Salmonella Enteritidis ( S . Enteritidis) are a significant threat to human health and poultry enterprises. Outer membrane vesicles (OMVs), which are naturally secreted by gram-negative bacteria, could be a good vaccine option because they have many biologically active substances, including lipopolysaccharides (LPS), outer membrane proteins (OMPs), and phospholipids, as well as periplasmic components. In the present study, we purified OMVs derived from S . Enteritidis and analyzed their characteristics through silver staining and sodium dodecyl sulfate polyacrylamide gel electrophoresis. In total, 108 proteins were identified in S . Enteritidis OMVs through liquid chromatography tandem mass spectrometry analysis, and OMPs, periplasmic proteins, and extracellular proteins (49.9% of total proteins) were found to be enriched in the OMVs compared with bacterial cells. Furthermore, native OMVs used in immunizations by either the intranasal route or the intraperitoneal route could elicit significant humoral and mucosal immune responses and provide strong protective efficiency against a lethal dose (~100-fold LD 50 ) of the wild-type S . Enteritidis infection. These results indicated that S . Enteritidis OMVs might be an ideal vaccine strategy for preventing S . Enteritidis diseases.

Characterization and analysis of the molecular weight of lignin for biorefining studies

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

Tolbert, Allison; Akinosho, Hannah; Khunsupat, Ratayakorn

2014-06-04

The molecular weight of lignin is a fundamental property that infl uences the recalcitrance of biomass and the valorization of lignin. The determination of the molecular weight of lignin in native biomass is dependent on the bioresources used and the isolation and purifi cation procedures employed. The three most commonly employed isolation methods are milled wood lignin (MWL), cellulolytic enzyme lignin (CEL), and enzymatic mild acidolysis lignin (EMAL). Common characterization techniques for determining the molecular weight of lignin will be addressed, with an emphasis on gel permeation chromatography (GPC). This review also examines the mechanisms behind several biological, physical, andmore » chemical pre-treatments and their impact on the molecular weight of lignin. The number average molecular weight (Mn), weight average molecular weight (Mw) and polydispersity index (D) all vary in magnitude depending on the biomass source, pre-treatment conditions, and isolation method. Additionally, there is a growing body of literature that supports changes in the molecular weight of lignin in response to genetic modifi cations in the lignin biosynthetic pathways. This review summarizes different procedures for obtaining the molecular weight of lignin that have been used in recent years and highlight future opportunities for applications of lignin.« less

Intracellular NADPH Levels Affect the Oligomeric State of the Glucose 6-Phosphate Dehydrogenase

PubMed Central

Tramonti, Angela; Lanini, Claudio; Cialfi, Samantha; De Biase, Daniela; Falcone, Claudio

2012-01-01

In the yeast Kluyveromyces lactis, glucose 6-phosphate dehydrogenase (G6PDH) is detected as two differently migrating forms on native polyacrylamide gels. The pivotal metabolic role of G6PDH in K. lactis led us to investigate the mechanism controlling the two activities in respiratory and fermentative mutant strains. An extensive analysis of these mutants showed that the NAD+(H)/NADP+(H)-dependent cytosolic alcohol (ADH) and aldehyde (ALD) dehydrogenase balance affects the expression of the G6PDH activity pattern. Under fermentative/ethanol growth conditions, the concomitant activation of ADH and ALD activities led to cytosolic accumulation of NADPH, triggering an alteration in the oligomeric state of the G6PDH caused by displacement/release of the structural NADP+ bound to each subunit of the enzyme. The new oligomeric G6PDH form with faster-migrating properties increases as a consequence of intracellular redox unbalance/NADPH accumulation, which inhibits G6PDH activity in vivo. The appearance of a new G6PDH-specific activity band, following incubation of Saccharomyces cerevisiae and human cellular extracts with NADP+, also suggests that a regulatory mechanism of this activity through NADPH accumulation is highly conserved among eukaryotes. PMID:23064253

pH shift protein recovery with organic acids on texture and color of cooked gels.

PubMed

Paker, Ilgin; Beamer, Sarah; Jaczynski, Jacek; Matak, Kristen E

2015-01-01

Isoelectric solubilization and precipitation (ISP) processing uses pH shifts to separate protein from fish frames, which may increase commercial interest for silver carp. Texture and color properties of gels made from silver carp protein recovered at different pH strategies and organic acid types were compared. ISP was applied to headed gutted silver carp using 10 mol L(-1) sodium hydroxide (NaOH) and either glacial acetic acid (AA) or a (1:1) formic and lactic acid combination (F&L). Protein gels were made with recovered protein and standard functional additives. Texture profile analysis and the Kramer shear test showed that protein gels made from protein solubilized at basic pH values were firmer, harder, more cohesive, gummier and chewier (P < 0.05) than proteins solubilized under acidic conditions. Acidic solubilization led to whiter (P < 0.05) gels, and using F&L during ISP yielded whiter gels under all treatments (P < 0.05). Gels made from ISP-recovered silver carp protein using organic acids show potential for use as a functional ingredient in restructured foods. © 2014 Society of Chemical Industry.

Energy-Efficient Bioalcohol Recovery by Gel Stripping

NASA Astrophysics Data System (ADS)

Godbole, Rutvik; Ma, Lan; Hedden, Ronald

2014-03-01

Design of energy-efficient processes for recovering butanol and ethanol from dilute fermentations is a key challenge facing the biofuels industry due to the high energy consumption of traditional multi-stage distillation processes. Gel stripping is an alternative purification process by which a dilute alcohol is stripped from the fermentation product by passing it through a packed bed containing particles of a selectively absorbent polymeric gel material. The gel must be selective for the alcohol, while swelling to a reasonable degree in dilute alcohol-water mixtures. To accelerate materials optimization, a combinatorial approach is taken to screen a matrix of copolymer gels having orthogonal gradients in crosslinker concentration and hydrophilicity. Using a combination of swelling in pure solvents, the selectivity and distribution coefficients of alcohols in the gels can be predicted based upon multi-component extensions of Flory-Rehner theory. Predictions can be validated by measuring swelling in water/alcohol mixtures and conducting h HPLC analysis of the external liquid. 95% + removal of butanol from dilute aqueous solutions has been demonstrated, and a mathematical model of the unsteady-state gel stripping process has been developed. NSF CMMI Award 1335082.

Sol-gel immobilized short-chain poly(ethylene glycol) coating for capillary microextraction of underivatized polar analytes.

PubMed

Kulkarni, Sameer; Shearrow, Anne M; Malik, Abdul

2007-12-07

Sol-gel coating with covalently bonded low-molecular-weight (MW<300 Da) poly(ethylene glycol) (PEG) chains was developed for capillary microextraction (CME). The sol-gel chemistry proved effective in the immobilization of low-molecular-weight PEGs thanks to the formation of chemical bonds between the organic-inorganic hybrid sol-gel PEG coating and the fused silica capillary inner surface. This chemical anchorage provided excellent thermal and solvent stability to the created sol-gel PEG coating as is evidenced by its high upper limit of allowable conditioning temperature (340 degrees C) and its practically identical performance before and after rinsing with various solvents. The prepared sol-gel PEG coating provided simultaneous extraction of moderately polar and highly polar analytes from aqueous samples without requiring derivatization, pH adjustment or salting-out procedures. Detection limits on the order of nanogram per liter (ng/L) were achieved in CME-GC-flame ionization detection experiments designed for the preconcentration and trace analysis of both highly polar and moderately polar compounds extracted directly from aqueous media using sol-gel short-chain PEG coated microextraction capillaries.

Hydroxyapatite, fluor-hydroxyapatite and fluorapatite produced via the sol-gel method: dissolution behaviour and biological properties after crystallisation.

PubMed

Tredwin, Christopher J; Young, Anne M; Abou Neel, Ensanya A; Georgiou, George; Knowles, Jonathan C

2014-01-01

Hydroxyapatite (HA), fluor-hydroxyapatite (FHA) with varying levels of fluoride ion substitution and fluorapatite (FA) were synthesised by the sol-gel method as possible implant coating or bone-grafting materials. Calcium nitrate and triethyl phosphite were used as precursors under an ethanol-water based solution. Different amounts of ammonium fluoride were incorporated for the preparation of the FHA and FA sol-gels. After heating and powdering the sol-gels, dissolution behaviour was assessed using ion chromatography to measure Ca(2+) and PO4 (3-) ion release. Biological behaviour was assessed using cellular proliferation with human osteosarcoma cells and alamarBlue™ assay. Statistical analysis was performed with a two way analysis of variance and post hoc testing with a Bonferroni correction. Increasing fluoride substitution into an apatite structure decreased the dissolution rate. Increasing the firing temperature of the HA, FHA and FA sol-gels up to 1,000 °C decreased the dissolution rate. There was significantly higher cellular proliferation on highly substituted FHA and FA than on HA or Titanium. The properties of an implant coating or bone grafting material can be tailored to meet specific requirements by altering the amount of fluoride that is incorporated into the original apatite structure. The dissolution behaviour can further be altered by the temperature at which the sol-gel is fired.

Kefiran-alginate gel microspheres for oral delivery of ciprofloxacin.

PubMed

Blandón, Lina M; Islan, German A; Castro, Guillermo R; Noseda, Miguel D; Thomaz-Soccol, Vanete; Soccol, Carlos R

2016-09-01

Ciprofloxacin is a broad-spectrum antibiotic associated with gastric and intestinal side effects after extended oral administration. Alginate is a biopolymer commonly employed in gel synthesis by ionotropic gelation, but unstable in the presence of biological metal-chelating compounds and/or under dried conditions. Kefiran is a microbial biopolymer able to form gels with the advantage of displaying antimicrobial activity. In the present study, kefiran-alginate gel microspheres were developed to encapsulate ciprofloxacin for antimicrobial controlled release and enhanced bactericidal effect against common pathogens. Scanning electron microscopy (SEM) analysis of the hybrid gel microspheres showed a spherical structure with a smoother surface compared to alginate gel matrices. In vitro release of ciprofloxacin from kefiran-alginate microspheres was less than 3.0% and 5.0% at pH 1.2 (stomach), and 5.0% and 25.0% at pH 7.4 (intestine) in 3 and 21h, respectively. Fourier transform infrared spectroscopy (FTIR) of ciprofloxacin-kefiran showed the displacement of typical bands of ciprofloxacin and kefiran, suggesting a cooperative interaction by hydrogen bridges between both molecules. Additionally, the thermal analysis of ciprofloxacin-kefiran showed a protective effect of the biopolymer against ciprofloxacin degradation at high temperatures. Finally, antimicrobial assays of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella typhymurium, and Staphylococcus aureus demonstrated the synergic effect between ciprofloxacin and kefiran against the tested microorganisms. Copyright © 2016 Elsevier B.V. All rights reserved.

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

What, How and Why? A Multi-Dimensional Case Analysis of the Challenges Facing Native and Non- Native EFL Teachers

ERIC Educational Resources Information Center

Demir, Yusuf

2017-01-01

On a multifaceted basis, this paper explores the challenges experienced by native and non-native English language teachers (NESTs and NNESTs) in a tertiary-level EFL setting in Turkey. Adopting a qualitative case study design, the data were gathered from five NESTs through interviews and from five NNESTs through hand-written accounts based on the…

Influence of the collection tube on metabolomic changes in serum and plasma.

PubMed

López-Bascón, M A; Priego-Capote, F; Peralbo-Molina, A; Calderón-Santiago, M; Luque de Castro, M D

2016-04-01

Major threats in metabolomics clinical research are biases in sampling and preparation of biological samples. Bias in sample collection is a frequently forgotten aspect responsible for uncontrolled errors in metabolomics analysis. There is a great diversity of blood collection tubes for sampling serum or plasma, which are widely used in metabolomics analysis. Most of the existing studies dealing with the influence of blood collection on metabolomics analysis have been restricted to comparison between plasma and serum. However, polymeric gel tubes, which are frequently proposed to accelerate the separation of serum and plasma, have not been studied. In the present research, samples of serum or plasma collected in polymeric gel tubes were compared with those taken in conventional tubes from a metabolomics perspective using an untargeted GC-TOF/MS approach. The main differences between serum and plasma collected in conventional tubes affected to critical pathways such as the citric acid cycle, metabolism of amino acids, fructose and mannose metabolism and that of glycerolipids, and pentose and glucuronate interconversion. On the other hand, the polymeric gel only promoted differences at the metabolite level in serum since no critical differences were observed between plasma collected with EDTA tubes and polymeric gel tubes. Thus, the main changes were attributable to serum collected in gel and affected to the metabolism of amino acids such as alanine, proline and threonine, the glycerolipids metabolism, and two primary metabolites such as aconitic acid and lactic acid. Therefore, these metabolite changes should be taken into account in planning an experimental protocol for metabolomics analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Design and Evaluation of Topical Diclofenac Sodium Gel Using Hot Melt Extrusion Technology as a Continuous Manufacturing Process with Kolliphor® P407.

PubMed

Pawar, Jaywant; Narkhede, Rajkiran; Amin, Purnima; Tawde, Vaishali

2017-08-01

The aim of the present context was to develop and evaluate a Kolliphor® P407-based transdermal gel formulation of diclofenac sodium by hot melt extrusion (HME) technology; central composite design was used to optimize the formulation process. In this study, we have explored first time ever HME as an industrially feasible and continuous manufacturing technology for the manufacturing of gel formulation using Kolliphor® P407 and Kollisolv® PEG400 as a gel base. Diclofenac sodium was used as a model drug. The HME parameters such as feeding rate, screw speed, and barrel temperature were crucial for the semisolid product development, and were optimized after preliminary trials. For the processing of the gel formulation by HME, a modified screw design was used to obtain a uniform product. The obtained product was evaluated for physicochemical characterization such as differential scanning calorimetry (DSC), X-ray diffraction (XRD), pH measurement, rheology, surface tension, and texture profile analysis. Moreover, it was analyzed for general appearance, spreadibility, surface morphology, and drug content. The optimized gel formulation showed homogeneity and transparent film when applied on a glass slide under microscope, pH was 7.02 and uniform drug content of 100.04 ± 2.74 (SD = 3). The DSC and XRD analysis of the HME gel formulation showed complete melting of crystalline API into an amorphous form. The Kolliphor® P407 and Kollisolv® PEG400 formed excellent gel formulation using HME with consistent viscoelastic properties of the product. An improved drug release was found for the HME gel, which showed a 100% drug release than that of a marketed product which showed only 88% of drug release at the end of 12 h. The Flux value of the HME gel was 106 than that of a marketed formulation, which showed only about 60 value, inferring a significant difference (P < 0.05) at the end of 1 h. This study demonstrates a novel application of the hot melt extrusion process for manufacturing of topical semisolid products.

Aligning Goals, Assessments, and Activities: An Approach to Teaching PCR and Gel Electrophoresis

PubMed Central

Robertson, Amber L.; Batzli, Janet; Harris, Michelle; Miller, Sarah

2008-01-01

Polymerase chain reaction (PCR) and gel electrophoresis have become common techniques used in undergraduate molecular and cell biology labs. Although students enjoy learning these techniques, they often cannot fully comprehend and analyze the outcomes of their experiments because of a disconnect between concepts taught in lecture and experiments done in lab. Here we report the development and implementation of novel exercises that integrate the biological concepts of DNA structure and replication with the techniques of PCR and gel electrophoresis. Learning goals were defined based on concepts taught throughout the cell biology lab course and learning objectives specific to the PCR and gel electrophoresis lab. Exercises developed to promote critical thinking and target the underlying concepts of PCR, primer design, gel analysis, and troubleshooting were incorporated into an existing lab unit based on the detection of genetically modified organisms. Evaluative assessments for each exercise were aligned with the learning goals and used to measure student learning achievements. Our analysis found that the exercises were effective in enhancing student understanding of these concepts as shown by student performance across all learning goals. The new materials were particularly helpful in acquiring relevant knowledge, fostering critical-thinking skills, and uncovering prevalent misconceptions. PMID:18316813

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

Morandeau, Antoine E.; White, Claire E.

Calcium–silicate–hydrate (C–S–H) gel is the main binder component in hydrated ordinary Portland cement (OPC) paste, and is known to play a crucial role in the carbonation of cementitious materials, especially for more sustainable alternatives containing supplementary cementitious materials. However, the exact atomic structural changes that occur during carbonation of C–S–H gel remain unknown. Here, we investigate the local atomic structural changes that occur during carbonation of a synthetic calcium–silicate–hydrate gel exposed to pure CO₂ vapour, using in situ X-ray total scattering measurements and subsequent pair distribution function (PDF) analysis. By analysing both the reciprocal and real-space scattering data as themore » C–S–H carbonation reaction progresses, all phases present during the reaction (crystalline and non-crystalline) have been identified and quantified, with the results revealing the emergence of several polymorphs of crystalline calcium carbonate (vaterite and calcite) in addition to the decalcified C–S–H gel. Furthermore, the results point toward residual calcium being present in the amorphous decalcified gel, potentially in the form of an amorphous calcium carbonate phase. As a result of the quantification process, the reaction kinetics for the evolution of the individual phases have been obtained, revealing new information on the rate of growth/dissolution for each phase associated with C–S–H gel carbonation. Moreover, the investigation reveals that the use of real space diffraction data in the form of PDFs enables more accurate determination of the phases that develop during complex reaction processes such as C–S–H gel carbonation in comparison to the conventional reciprocal space Rietveld analysis approach.« less

Confocal Raman spectroscopy: In vivo biochemical changes in the human skin by topical formulations under UV radiation.

PubMed

Tosato, M G; Orallo, D E; Ali, S M; Churio, M S; Martin, A A; Dicelio, L

2015-12-01

A new approach to the study of the effects on human skin of mycosporine-like amino acids (MAAs) and gadusol (Gad) incorporated in polymer gel is proposed in this work. The depth profile and photoprotector effects of Pluronic F127® gels containing each of the natural actives were evaluated by in vivo confocal Raman spectroscopy aiming at the analysis of the biochemical changes on human skin. Hierarchical cluster analysis (HCA) showed that the data corresponding to different depths of the skin, from surface to 4 μm, and from 6 to 16 μm, remained in the same cluster. In vivo Raman spectra, classified into five different layers of epidermis according to their similarities, indicated that the amount of Gad gel increased by about 26% in the outermost layer of the stratum corneum (SC) and that MAAs gel at 2 μm depth was 103.4% higher than in the outermost layer of the SC. Variations in the SC of urocanic acid at 1490-1515 cm(-1) and 1652 cm(-1) and histidine at 1318 cm(-1) were calculated, before and after UV exposure with or without gels. With the application of gels the vibrational modes that correspond to lipids in trans conformation (1063 and 1128 cm(-1)) increased with respect to normal skin, whereas gauche conformation (1085 cm(-1)) disappeared. Our studies suggest that gels protected the skin against the stress of the natural defense mechanism caused by high levels of UV exposure. Copyright © 2015 Elsevier B.V. All rights reserved.

Pulsed-field gel electrophoresis typing of Staphylococcus aureus isolates

USDA-ARS?s Scientific Manuscript database

Pulsed-field gel electrophoresis (PFGE) is the most applied and effective genetic typing method for epidemiological studies and investigation of foodborne outbreaks caused by different pathogens, including Staphylococcus aureus. The technique relies on analysis of large DNA fragments generated by th...

Selection and differentiation of Bacillus spp. Antagonistic to Fusarium oxysporum f.sp. lycopersici and Alternaria solani infecting Tomato.

PubMed

Shanmugam, Veerubommu; Atri, Kamini; Gupta, Samriti; Kanoujia, Nandina; Naruka, Digvijay Singh

2011-03-01

Antagonistic Bacillus spp. displaying in vitro production of siderophore, chitinase, and β-1,3-glucanase were identified from dual culture assays. In independent greenhouse studies, seed bacterization and soil application of Bacillus atrophaeus S2BC-2 challenge inoculated with Fusarium oxysporum f.sp. lycopersici (FOL) and Alternaria solani (AS) recorded low percent disease index of 25.3 and 28.7, respectively, over nonbacterised pathogen control (44.3 and 56.4). The low disease incidence corroborated with tomato growth promotion with high vigor index (8,041.2) and fresh plant weight (82.5 g) on challenge inoculation with FOL. Analysis of root and leaf samples in rhizobacterial treatment challenged with FOL and AS revealed maximum induction of chitinase (1.9 and 1.7 U/mg of protein, respectively) and β-1,3-glucanase (23.5 and 19.2 U/mg of protein, respectively). In native gel activity assays, the rhizobacterial treatment on challenge inoculation strongly expressed three high intensity PO isoforms along with one low intensity isoform. In studies on genetic diversity of the Bacillus strains by repetitive extragenomic palindromic-polymerase chain reaction (REP-PCR) and amplified rDNA restriction analysis (ARDRA) patterns, ARDRA was more highly discriminant than REP-PCR and allowed grouping of the strains and differentiation of the antagonistic strains from other isolates.

Lead and ethanol co-exposure lead to blood oxidative stress and subsequent neuronal apoptosis in rats.

PubMed

Flora, Swaran J S; Gautam, Pratibha; Kushwaha, Pramod

2012-01-01

The present study was aimed at investigating chronic exposure to lead and ethanol, individually and in combination with blood oxidative stress leading to possible brain apoptosis in rats. Rats were exposed to lead (0.1% w/v in drinking water) or ethanol (1 and 10%) either individually or in combination for four months. Biochemical variables indicative of oxidative stress (blood and brain) and brain apoptosis were examined. Native polyacrylamide agarose gel electrophoresis was carried out in brain homogenates for glucose-6-phosphate dehydrogenase (G6PD) analysis, whereas western blot analysis was done for the determination of apoptotic markers like Bax, Bcl-2, caspase-3, cytochrome c and p53. The results suggest that most pronounced increase in oxidative stress in red blood cells and brain of animals co-exposed to lead and 10% ethanol compared all the other groups. Decrease in G6PD activity followed the same trend. Upregulation of Bax, cytochrome c, caspase-3, p53 and down-regulation of Bcl-2 suggested apoptosis in the rat brain co-exposed to lead and ethanol (10%) compared with their individual exposures. Significantly high lead accumulation in blood and brain during co-exposure further support synergistic toxicity. The present study thus suggests that higher consumption of ethanol during lead exposure may lead to brain apoptosis, which may be mediated through oxidative stress.

Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico.

PubMed

Martínez-Cruzado, J C; Toro-Labrador, G; Ho-Fung, V; Estévez-Montero, M A; Lobaina-Manzanet, A; Padovani-Claudio, D A; Sánchez-Cruz, H; Ortiz-Bermúdez, P; Sánchez-Crespo, A

2001-08-01

To estimate the maternal contribution of Native Americans to the human gene pool of Puerto Ricans--a population of mixed African, European, and Amerindian ancestry--the mtDNAs of two sample sets were screened for restriction fragment length polymorphisms (RFLPs) defining the four major Native American haplogroups. The sample set collected from people who claimed to have a maternal ancestor with Native American physiognomic traits had a statistically significant higher frequency of Native American mtDNAs (69.6%) than did the unbiased sample set (52.6%). This higher frequency suggests that, despite the fact that the native Taíno culture has been extinct for centuries, the Taíno contribution to the current population is considerable and some of the Taíno physiognomic traits are still present. Native American haplogroup frequency analysis shows a highly structured distribution, suggesting that the contribution of Native Americans foreign to Puerto Rico is minimal. Haplogroups A and C cover 56.0% and 35.6% of the Native American mtDNAs, respectively. No haplogroup D mtDNAs were found. Most of the linguistic, biological, and cultural evidence suggests that the Ceramic culture of the Taínos originated in or close to the Yanomama territory in the Amazon. However, the absence of haplogroup A in the Yanomami suggests that the Yanomami are not the only Taíno ancestors.

Interaction of partially denatured insulin with a DSPC floating lipid bilayer.

PubMed

Dennison, A J C; Jones, R A L; Staniforth, R A; Parnell, A J

2016-01-21

The carefully controlled permeability of cellular membranes to biological molecules is key to life. In degenerative diseases associated with protein misfolding and aggregation, protein molecules or their aggregates are believed to permeate these barriers and threaten membrane integrity. We used neutron reflectivity to study the interaction of insulin, a model amyloidogenic protein, with a DSPC floating lipid bilayer. Structural changes consistent with protein partitioning to the membrane interior and adsorption to a gel phase model lipid bilayer were observed under conditions where the native fold of the protein is significantly destabilised. We propose that the perturbation of the membrane by misfolded proteins involves long term occupation of the membrane by these proteins, rather than transient perforation events.

Sequences with high propensity to form G-quartet structures in kinetoplast DNA from Phytomonas serpens.

PubMed

Sá-Carvalho, D; Traub-Cseko, Y M

1995-06-01

Naturally occurring sequences containing repetitive guanine motifs have the potential to form tetraplex DNA. Phytomonas serpens minicircle DNA shows some regions where one strand is composed mainly of G and T (GT regions). These regions contain several stretches of contiguous guanines. An oligonucleotide was constructed with the sequence corresponding to one of these regions (Phyto-GT). It was demonstrated by native gel electrophoresis and methylation protection that Phyto-GT forms tetramolecular (G4), bimolecular (G'2) and unimolecular (G4') structures stabilized through G-quartets. Tetraplex DNA formation by this sequence could have biological relevance as it can be formed in physiological conditions and GT regions comprise approximately one-third of P. serpens and Crithidia oncopelti minicircles.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Improved gel electrophoresis matrix for hydrophobic protein separation and identification.

PubMed

Tokarski, Caroline; Fillet, Marianne; Rolando, Christian

2011-03-01

We propose an improved acrylamide gel for the separation of hydrophobic proteins. The separation strategy is based on the incorporation of N-alkylated and N,N'-dialkylated acrylamide monomers in the gel composition in order to increase hydrophobic interactions between the gel matrix and the membrane proteins. Focusing on the most efficient monomer, N,N'-dimethylacrylamide, the potentiality of the new matrix was evaluated on membrane proteins of the human colon HCT-116 cell line. Protein analysis was performed using an adapted analytical strategy based on FT-ICR tandem mass spectrometry. As a result of this comparative study, including advanced reproducibility experiments, more hydrophobic proteins were identified in the new gel (average GRAVY: -0.085) than in the classical gel (average GRAVY: -0.411). Highly hydrophobic peptides were identified reaching a GRAVY value up to 1.450, therefore indicating their probable locations in the membrane. Focusing on predicted transmembrane domains, it can be pointed out that 27 proteins were identified in the hydrophobic gel containing up to 11 transmembrane domains; in the classical gel, only 5 proteins containing 1 transmembrane domain were successfully identified. For example, multiple ionic channels and receptors were characterized in the hydrophobic gel such as the sodium/potassium channel and the glutamate or the transferrin receptors whereas they are traditionally detected using specific enrichment techniques such as immunoprecipitation. In total, membrane proteins identified in the classical gel are well documented in the literature, while most of the membrane proteins only identified on the hydrophobic gel have rarely or never been described using a proteomic-based approach. 2010 Elsevier Inc. All rights reserved.

Optimal imaging and analysis of human vaginal coating by drug delivery gels

PubMed Central

Henderson, Marcus H; Couchman, Grace M; Walmer, David K; Peters, Jennifer J; Owen, Derek H; Brown, Matthew A; Lavine, Michael L; Katz, David F

2007-01-01

Objective We used a new optical imaging technique to compare human intravaginal coating distributions of Conceptrol® and Advantage™. These gels are surrogates for future microbicidal gels, differing in molecular structures and biophysical properties. Methods For each protocol, a 3-mL gel bolus was inserted to the posterior fornix while the woman was in the supine position. She then either: (1) remained supine (10 min); or (2) sat up (1 min), stood up (1 min), sat down (1 min), and returned to supine for a net elapsed time of 10 min. The imaging device is sized/shaped like a phallus, and measurements while the device was inserted provide data that simulate peri-intromission coating. Results Coating by Advantage™ was more extensive and uniform than coating by Conceptrol®, with smaller bare spots of uncoated epithelium. Change in posture tended to increase extent and uniformity of coating, details differing between gels. Conclusions Results are consistent with predictions of mechanistic coating theory, using gel rheological data as inputs. PMID:17241845

Pozzolanic activity and durability of nano silica, micro silica and silica gel contained concrete

NASA Astrophysics Data System (ADS)

Al Ghabban, Ahmed; Al Zubaidi, Aseel B.; Fakhri, Zahraa

2018-05-01

This paper aims to investigate the influence of replacement of cement with nano silica, micro silica and silica gel admixtures on pozzolanic activity, the replacement ratio was10% for all admixture, silica gel used in two forms (beads and crushed powder). Also, the water absorption test was investigated for obtaining the durability properties of concrete, in specimens for this test admixtures were added in four different dosages 1%, 2%, 3% and 4% by weight of the cementitious material into the concrete mixture. Experimental investigations of modified concrete were conducted after 28 days of water curing. Results showed that mixes of nano silica and crushed silica gel showed a higher pozzolanic activity index. For the water absorption test, all mixes incorporating nano silica, micro silica and silica gel showed lower absorption than control mixes best result were noticed with crushed silica gel and nano silica mixes. DTA analysis confirms the results for both poisonous activity and water absorption.

Crosslinking of polysaccharides in room temperature ionic liquids by ionizing radiation

NASA Astrophysics Data System (ADS)

Kimura, Atsushi; Nagasawa, Naotsugu; Shimada, Akihiko; Taguchi, Mitsumasa

2016-07-01

Crosslinking of polysaccharides in room temperature ionic liquids (RTILs) by ionizing radiation were investigated by the scavenging method, fluorescent and X-ray photoelectron spectroscopy (XPS) analysis. Radiation chemical yields of hydroxyl radicals inducing the crosslinking of cellulose were estimated with phenol as a scavenger, and increased with water content in 1-ethyl-3-methylimidazolium acetate (EMI-acetate). Cellulose gel was also produced in fluorescent carboxylate-based RTILs, 1,3-dibutylimidazolium acetate (DBI-acetate). Light emission from DBI-acetate in cellulose gel was observed and 20-nm red shifted at a maximum wavelength of 415 nm when excited at 323 nm. Expected elements of carbon and oxygen were detected in neat cellulose by XPS, while additional nitrogen was detected in radiation-crosslinked cellulose gel produced in EMI-acetate. These results indicate that RTILs is incorporated in the cellulose gel. Chitin gel was first obtained in 1-butyl-3-methyimidazolium chloride by γ-ray irradiations, and its gel fraction increased with the dose and reached 86% at 60 kGy.

Invasive non-native plants have a greater effect on neighbouring natives than other non-natives.

PubMed

Kuebbing, Sara E; Nuñez, Martin A

2016-09-12

Human activity is creating a global footprint by changing the climate, altering habitats and reshuffling the distribution of species. The movement of species around the globe has led to the naturalization and accumulation of multiple non-native species within ecosystems, which is frequently associated with habitat disturbance and changing environmental conditions. However, interactions among species will also influence community composition, but little is known about the full range of direct and indirect interactions among native and non-native species. Here, we show through a meta-analysis of 1,215 pairwise plant interactions between 274 vascular plant species in 21 major habitat types that interactions between non-native plants are asymmetrical with interactions between non-native and native plants. Non-native plants were always bad neighbours, but the negative effect of non-natives on natives was around two times greater than the effect of non-natives on other non-natives. In contrast, the performance of non-native plants was five times higher in the presence of a neighbouring native plant species than in the presence of a neighbouring non-native plant species. Together, these results demonstrate that invaded plant communities may accumulate additional non-native species even if direct interactions between non-natives species are negative. Put another way, invasions may be more likely to lead to more invasions, requiring more active management of ecosystems by promoting native species restoration to undermine invasive positive feedback and to assist native species recovery in invaded ecosystems.

Investigation of novel sol-gel hydrophobic surfaces for desorption electrospray ionization-mass spectrometry analysis.

PubMed

Penna, Andrea; Elviri, Lisa; Careri, Maria; Mangia, Alessandro; Predieri, Giovanni

2011-05-01

Sol-gel-based materials were synthesized, characterized and finally tested as solid supports for desorption electrospray ionization-mass spectrometry (DESI-MS) analysis of a mixture of compounds of different polarity. Films with thickness in the 2-4 μm range were obtained by a dip-coating process using tetraethoxysilane (TEOS) and octyltriethoxysilane (OTES) as sol-gel precursors. Three types of surface with different hydrophobic character were obtained by varying the TEOS/OTES ratio in the sol-gel mixture. Each coating was characterized by atomic force microscopy investigations, gaining insight into homogeneity, smoothness and thickness of the obtained films. To study hydrophobicity of each surface, surface free energy measurements were performed. Different DESI-MS responses were observed when different solvent mixture deposition procedures and solvent spray compositions were investigated. Results were finally compared to those obtained by using commercial polytetrafluoroethylene-coated slides. It was found that surface free energy plays an important role in the desorption/ionization process as a function of the polarity of analytes.