Sample records for in-capillary denaturing polymer

  1. RNA separation by in-capillary denaturing polymer electrophoresis with 1,2,5-thiadiazole as an additive. (United States)

    Sumitomo, Keiko; Yamaguchi, Yoshinori; Tatsuta, Kuniaki


    1,2,5-Thiadiazole improved RNA separation with in-capillary denaturing polymer electrophoresis. 1,2,5-Thiadiazole was synthesized as an extraction solvent substituted for a halogenated solvent. While 1,2,5-thiadiazole was an excellent extraction solvent and an environmentally friendly solvent, we found that 1,2,5-thiadiazole was a strong hydrophobic compound for RNA and the RNA separation performance by in-capillary denaturing polymer electrophoresis was dramatically improved. We suggest "in-capillary denaturing polymer electrophoresis" as an RNA separation that realizes the denaturing and separation simultaneously. RNA separation by the method required a strong denaturant, acetic acid, to cleave the intramolecular hydrogen. The running buffer containing acetic acid was of high conductivity and low pH, in which the condition introduced Joule heating and low sensitivity. While conventional denaturants, formaldehyde and urea, maintained small electric conductivity and neutral pH, these denaturants were too weak to achieve the RNA separation by in-capillary denaturing polymer electrophoresis. 1,2,5-Thiadiazole being a neutral molecule, both conductivity and buffer pH were able to be adjusted to a desirable strength for RNA separation. In this paper, we report that RNA separation by in-capillary denaturing polymer electrophoresis in neutral pH was achieved and the sensitivity for RNA separation was higher than that for RNA separation by in-capillary denaturing polymer electrophoresis with acetic acid. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Acetic acid denaturing for RNA capillary polymer electrophoresis. (United States)

    Sumitomo, Keiko; Sasaki, Motoyasu; Yamaguchi, Yoshinori


    A strong denaturant to cleave intramolecular hydrogen bonds in RNA is required for RNA size separation in a small sample volume (RNA and the RNA separation performance was dramatically improved by capillary electrophoresis with a sieving matrix containing acetic acid. We revealed that the denaturing ability of 2.0 M acetic acid was stronger than that of either 2.5 M formaldehyde or 7.0 M urea by estimating DNA melting temperature. Consequently, we suggested "in-capillary denaturing polymer electrophoresis" as the RNA size separation methodology to simultaneously denature and separate RNA in a small sample volume without conventional in vitro sample preparation before electrophoresis. The baseline separation of RNA with a size of 100-10,000 nt was achieved in 25 min by "in-capillary denaturing polymer electrophoresis" with the running buffer containing 2.0 M acetic acid. The resolution and the theoretical plates of RNA separation peaks were larger than those of the RNA separation in a conventional CGE with in vitro sample preparation by 7.0 M urea. In addition, we detected RNA peaks from the nucleic acids extracted from NIH 3T3 cells without DNase enzyme treatment.

  3. Molecular sieving polymer for DNA/RNA separation in capillary electrophoresis (United States)

    Liu, Chenchen; Yamaguchi, Yoshinori; Dou, Xiaoming


    In capillary polymer electrophoresis, the property of polymer sieving matrix dominates the migration behavior of DNA/RNA. We investigated the capillary electrophoresis of RNA ranging from 100 nt to 10,000 nt in polyacrylamide (PA) solutions with different molecular weights (Mw) and different concentrations. We observed that the resolution length (RSL) of RNA fragments was improved and the migration time was prolonged, when polymer concentration was increased. The resolution for small RNA fragments (3000 nt) became inseparable. In addition, we estimated the smallest resolvable nucleotide length (Ls) by the plot of RSL against RNA size.

  4. A water-soluble conjugated polymer for protein identification and denaturation detection. (United States)

    Xu, Qingling; Wu, Chunxian; Zhu, Chunlei; Duan, Xinrui; Liu, Libing; Han, Yuchun; Wang, Yilin; Wang, Shu


    Rapid and sensitive methods to detect proteins and protein denaturation have become increasingly needful in the field of proteomics, medical diagnostics, and biology. In this paper, we have reported the synthesis of a new cationic water-soluble conjugated polymer that contains fluorene and diene moieties in the backbone (PFDE) for protein identification by sensing an array of PFDE solutions in different ionic strengths using the linear discriminant analysis technique (LDA). The PFDE can form complexes with proteins by electrostatic and/or hydrophobic interactions and exhibits different fluorescence response. Three main factors contribute to the fluorescence response of PFDE, namely, the net charge density on the protein surface, the hydrophobic nature of the protein, and the metalloprotein characteristics. The denaturation of proteins can also be detected using PFDE as a fluorescent probe. The interactions between PFDE and proteins were also studied by dynamic light scattering (DLS) and isothermal titration microcalorimetry (ITC) techniques. In contrast to other methods based on conjugated polymers, the synthesis of a series of quencher or dye-labeled acceptors or protein substrates has been avoided in our method, which significantly reduces the cost and the synthetic complexity. Our method provides promising applications on protein identification and denaturation detection in a simple, fast, and label-free manner based on non-specific interaction-induced perturbation of PFDE fluorescence response.

  5. Facilitating protein denaturation in organic solvent and the contribution to the promoting dispersion of graphite nanoplatelets in a polymer

    Directory of Open Access Journals (Sweden)

    T. Liu


    Full Text Available Denatured proteins, natural macromolecules are very attractive for advanced nanocomposites owing to their multiple functional chemical groups. However, denaturation processes were only successfully conducted in an aqueous environment, limiting their broad applications in hydrophobic polymers. In this study, we report an effective approach of denaturing soy protein at nanoscale in an organic solvent. Further, the denatured soy protein was found to be able to infiltrate between the graphite nanoplatelet (GNP layers to reduce the thickness of GNPs and improve the dispersion of the nanoparticles in either the suspension or the final polymeric nanocomposites. As a result, remarkable improvements in transparency and electrical conductivity have been achieved for the nanocomposites with the GNPs treated by the denatured soy protein.

  6. Topographical properties of polymer films deposited in capillaries for electrophoretic separations of large organic molecules

    Czech Academy of Sciences Publication Activity Database

    Guryča, Vilém; Pacáková, V.; Tlusťáková, Marie; Štulík, K.; Michálek, Jiří


    Roč. 27, č. 13 (2004), s. 1121-1129 ISSN 1615-9306 R&D Projects: GA AV ČR IBS4050005; GA AV ČR KSK4055109 Institutional research plan: CEZ:AV0Z4050913 Keywords : capillary electrophoresis * hydrogel polymer coating * column technology Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.927, year: 2004

  7. Acetic acid denaturing pulsed field capillary electrophoresis for RNA separation. (United States)

    Li, Zhenqing; Dou, Xiaoming; Ni, Yi; Sumitomo, Keiko; Yamaguchi, Yoshinori


    Based on our previous work of in-capillary denaturing polymer electrophoresis, we present a study of RNA molecular separation up to 6.0 kilo nucleotide by pulsed field CE. This is the first systematic investigation of electrophoresis of a larger molecular mass RNA in linear hydroxyethylcellulose (HEC) under pulsed field conditions. The parameters that may influence the separation performance, e.g. gel polymer concentration, modulation depth and pulse frequency, are analyzed in terms of resolution and mobility. For denaturing and separating RNA in the capillary simultaneously, 2 M acetic acid was added into the HEC polymer to serve as separation buffer. Result shows that (i) in pulsed field conditions, RNA separation can be achieved in a wide range of concentration of HEC polymer, and RNA fragments between 0.3 and 0.6 kilo nucleotide are sensitive to the polymer concentration; (ii) under certain pulsed field conditions, RNA fragments move linearly as the modulation depth increases; (iii) 12.5 Hz is the resonance frequency for RNA reorientation time and applied frequency.

  8. Hand-held optical sensor using denatured antibody coated electro-active polymer for ultra-trace detection of copper in blood serum and environmental samples. (United States)

    Chandra, Sutapa; Dhawangale, Arvind; Mukherji, Soumyo


    An optimum copper concentration in environment is highly desired for all forms of life. We have developed an ultrasensitive copper sensor which functions from femto to micro molar concentration accurately (R 2 = 0.98). The sensor is based on denatured antibody immunoglobulin G (IgG), immobilized on polyaniline (PAni) which in turn is the coating on the core of an optical fiber. The sensing relies on changes in evanescent wave absorbance in the presence of the analyte. The sensor showed excellent selectivity towards Cu (II) ions over all other metal ions. The sensor was tested with lake and marine water samples to determine unknown concentrations of copper ions and the recovery results were within 90-115%, indicating reasonable accuracy. We further integrated the fiber-optic sensor with a miniaturized hand-held instrumentation platform to develop an accurate and field deployable device which can broadly be applicable to determine Cu (II) concentration in a wide range of systems - natural water bodies, soil as well as blood serum. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Determination of pore size distributions in capillary-channeled polymer fiber stationary phases by inverse size-exclusion chromatography and implications for fast protein separations. (United States)

    Wang, Zhengxin; Marcus, R Kenneth


    Capillary-channeled polymer (C-CP) fibers have been utilized as liquid chromatography stationary phases, primarily for biomacromolecule separations on the analytical and preparative scales. The collinear packing of the eight-channeled C-CP fibers provides for very efficient flow, allowing operation at high linear velocity (u>100mm s(-1)) and low backpressure (chromatography (iSEC) has been employed to determine the pore size distribution (PSD) within C-CP fibers. A diversity of test species (from metal ions to large proteins) was used as probes under non-retaining conditions to obtain a response curve reflecting the apparent partition coefficient (Kd) versus hydrodynamic radii (rm). A mean pore radius (rp) of 4.2nm with standard deviation (sp) of ±1.1nm was calculated by fitting the Kd versus rm data to model equations with a Gaussian pore size distribution, and a pore radius of 4.0±0.1nm was calculated based on a log-normal distribution. The derived mean pore radius is much smaller than traditional support materials, with the standard deviation showing a relatively uniform pore distribution. van Deemter plots were analyzed to provide practical confirmation of the structural implications. Large molecules (e.g., proteins) that are fully excluded from pores have no significant C-terms in the van Deemter plots whereas small molecules that can access the pore volumes display appreciable C-terms, as expected. Fitting of retention data to the Knox equation suggests that the columns operate with a characteristic particle diameter (dp) of ∼53μm. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. How adsorption influences DNA denaturation

    NARCIS (Netherlands)

    Allahverdyan, A.E.; Gevorkian, Z.S.; Hu, C.-K.; Nieuwenhuizen, T.M.


    The thermally induced denaturation of DNA in the presence of an attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the surface, the denaturation phase transition disappears. Instead,

  11. Denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    Kocherginskaya, S.A.; Cann, I.K.O.; Mackie, R.I.


    It is worthwhile considering that only some 30 species make up the bulk of the bacterial population in human faeces at any one time based on the classical cultivation-based approach. The situation in the rumen is similar. Thus, it is practical to focus on specific groups of interest within the complex community. These may be the predominant or the most active species, specific physiological groups or readily identifiable (genetic) clusters of phylogenetically related organisms. Several 16S rDNA fingerprinting techniques can be invaluable for selecting and monitoring sequences or phylogenetic groups of interest and are described below. Over the past few decades, considerable attention was focussed on the identification of pure cultures of microbes on the basis of genetic polymorphisms of DNA encoding rRNA such as ribotyping, amplified fragment length polymorphism and randomly amplified polymorphic DNA. However, many of these methods require prior cultivation and are less suitable for use in analysis of complex mixed populations although important in describing cultivated microbial diversity in molecular terms. Much less attention was given to molecular characterization of complex communities. In particular, research into diversity and community structure over time has been revolutionized by the advent of molecular fingerprinting techniques for complex communities. Denaturing or temperature gradient gel electrophoresis (DGGE/TGGE) methods have been successfully applied to the analysis of human, pig, cattle, dog and rodent intestinal populations

  12. 27 CFR 19.752 - Denaturation records. (United States)


    ... Denaturation records. (a) General. Each processor qualified to denature spirits shall maintain daily records of..., recovered denatured spirits, spirits residues, and articles redistilled in the processing account for...) Recovered denatured spirits or recovered articles received, restored, and/or redenatured; (7) Packages of...

  13. Denatured thorium cycle: an overview

    International Nuclear Information System (INIS)

    Sege, C.A.; Strauch, S.; Omberg, R.P.; Spiewak, I.


    We performed a scenario evaluation that delineates the potential role of denatured uranium/thorium-fueled reactors, including breeders, in symbiotic systems. In this study, reactors fueled with plutonium were built in secure centers, while reactors at dispersed sites were fueled with natural, low-enriched, or denatured uranium (12% 233 U or 20% 235 U in 238 U). The installed nuclear capacity is assumed to be 350 MW(electric) in the year 2000, with a net increase of 15 GW(electric)/y permitted through the year 2050. The U.S. Department of Energy Division of Uranium Resources and Enrichment projected the two bounding cases of uranium recoverable at a marginal cost of $160/lb U 3 O 8 or less used in this study. The marginal cost of $160/lb U 3 O 8 occurs at 3 million short tons (ST) for the high-cost supply and at 6 million ST for the intermediate-cost supply. For the assumed high-cost U 3 O 8 supply (3 million ST U 3 O 8 ), thermal recycle with denatured light water reactors (LWRs) will achieve the same incremental increase in maximum achievable nuclear capacity as U/Pu recycle in LWRs [approx. 200 GW(electric) more than once-through cycles]. Introduction of a breeder is required for the system to achieve the projected nuclear demand [1100 GW(clectric) in 2049]. For all denatured systems, including those with breeders, a significantly larger fraction of the installed capacity can be located at dispersed sites, compared with U/Pu systems. For the assumed intermediate-cost U 3 O 8 supply (6 million ST U 3 O 8 ), thermal recycle with advanced converters will permit projected nuclear demand to be met for both the Pu/U and denatured uranium--thorium cycles

  14. Microwave discharges in capillary tubes

    International Nuclear Information System (INIS)

    Dervisevic, Emil


    This research thesis aims at being a contribution to the study of microwave discharge by a surface wave, and more precisely focusses on the discharge in capillary tubes filled with argon. The author first present theoretical models which describe, on the one hand, the propagation of the surface wave along the plasma column, and, on the other hand, longitudinal and radial profiles of the main discharge characteristics. The second part addresses the study of the influence of parameters (gas pressure and tube radius) on discharge operation and characteristics. Laws of similitude as well as empirical relationships between argon I and argon II emission line intensities, electron density, and electric field in the plasma have been established [fr

  15. Paramecium swimming in capillary tube (United States)

    Jana, Saikat; Um, Soong Ho; Jung, Sunghwan


    Swimming organisms in their natural habitat need to navigate through a wide range of geometries and chemical environments. Interaction with boundaries in such situations is ubiquitous and can significantly modify the swimming characteristics of the organism when compared to ideal laboratory conditions. We study the different patterns of ciliary locomotion in glass capillaries of varying diameter and characterize the effect of the solid boundaries on the velocities of the organism. Experimental observations show that Paramecium executes helical trajectories that slowly transition to straight lines as the diameter of the capillary tubes decreases. We predict the swimming velocity in capillaries by modeling the system as a confined cylinder propagating longitudinal metachronal waves that create a finite pressure gradient. Comparing with experiments, we find that such pressure gradient considerations are necessary for modeling finite sized ciliary organisms in restrictive geometries.

  16. 27 CFR 19.456 - Adding denaturants. (United States)


    ... proprietor shall submit a flow diagram of the intended process or method of adding denaturants. (Sec. 201... OF THE TREASURY LIQUORS DISTILLED SPIRITS PLANTS Denaturing Operations and Manufacture of Articles...

  17. 27 CFR 19.454 - Gauge for denaturation. (United States)


    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Gauge for denaturation. 19... Denaturation § 19.454 Gauge for denaturation. The proprietor shall gauge spirits before denaturation and after denaturation and record each gauge on the record of denaturation as prescribed in § 19.752(b). However, spirits...

  18. Influence of Ficoll on urea induced denaturation of fibrinogen

    Directory of Open Access Journals (Sweden)

    Kamatchi Sankaranarayanan


    Full Text Available Ficoll is a neutral, highly branched polymer used as a molecular crowder in the study of proteins. Ficoll is also part of Ficoll-Paque used in biology laboratories to separate blood to its components (erythrocytes, leukocytes etc.,. Role of Ficoll in the urea induced denaturation of protein Fibrinogen (Fg has been analyzed using fluorescence, circular dichroism, molecular docking and interfacial studies. Fluorescence studies show that Ficoll prevents quenching of Fg in the presence of urea. From the circular dichroism spectra, Fg shows conformational transition to random coil with urea of 6 M concentration. Ficoll helps to shift this denaturation concentration to 8 M and thus constraints by shielding Fg during the process. Molecular docking studies indicate that Ficoll interacts favorably with the protein than urea. The surface tension and shear viscosity analysis shows clearly that the protein is shielded by Ficoll.

  19. Denaturation and electrophoresis of RNA with formaldehyde. (United States)

    Rio, Donald C


    Electrophoretic size fractionation can be used to denature and separate large mRNA molecules (0.5-10 kb) on formaldehyde-containing agarose gels. Formaldehyde contains a carbonyl group that reacts to form Schiff bases with the imino or amino groups of guanine, adenine, and cytosine. These covalent adducts prevent normal base pairing and maintain the RNA in a denatured state. Because these adducts are unstable, formaldehyde must be present in the gel to maintain the RNA in the denatured state. This protocol describes the preparation of an agarose gel with formaldehyde and its setup in a horizontal electrophoresis apparatus. RNA samples are prepared and denatured in a solution of formamide and formaldehyde and, with 0.5- to 10-kb size markers, subjected to electrophoresis through the gel. Following electrophoresis, the gel is stained to visualize RNA markers or rRNA using one of several different types of stains. © 2015 Cold Spring Harbor Laboratory Press.

  20. Denaturation and electrophoresis of RNA with glyoxal. (United States)

    Rio, Donald C


    This protocol is used to denature and separate large mRNA molecules (0.5-10 kb) on agarose gels by electrophoretic size fractionation. Glyoxal (also called diformyl or ethanedial), the agent responsible for maintaining denaturation in this protocol, contains two carbonyl groups that react to form a cyclic ring structure with the imino and amino groups of guanine. It can also react with the amino groups of adenine and cytidine. When RNA is denatured in the presence of glyoxal, this covalent adduct prevents normal base pairing and maintains the RNA in a denatured state in agarose gels. Once formed, these adducts are stable at room temperature at pH RNA in the denatured state. Because the fully denatured RNA migrates through agarose gels according to its molecular mass, this method can be used to accurately size mRNA molecules. Following electrophoresis and reversal of glyoxalation, the RNA can be detected using a northern hybridization procedure. © 2015 Cold Spring Harbor Laboratory Press.

  1. Electromigration behavior of nucleic acids in capillary electrophoresis under pulsed-field conditions. (United States)

    Li, Zhenqing; Liu, Chenchen; Dou, Xiaoming; Ni, Yi; Wang, Jiaxuan; Yamaguchi, Yoshinori


    We have presented a study focused on the migration pattern of double-stranded DNA (dsDNA) and RNA under pulsed field conditions. By calculating the dependence of nucleic acid mobility on its molecular size in a double logarithm plot, we found that (I) dsDNA molecules proceeded by a sigmoidal migration regime which was probably related to Ogston sieving, transition regime, and reptation model. Furthermore, the transition regime disappeared if DNA was resolved in a higher molecular mass HEC. (II) The migration pattern of RNA was relevant to the denaturant used for separation. When RNA was denatured by acetic acid, its mobility parabolically declined with its molecular size. The mobility was linearly decreased with the molecular size if urea was employed as denaturant. (III) RNA may migrate by Ogston, reptation without orientation mechanism when denatured by urea, whereas these two models were not suitable for RNA if denatured by acetic acid. Even though the electrophoretic conditions of PFCE were varied, the sigmoidal, linear, parabolic migration patterns could still be observed. (IV) Under certain modulation depth, the migration time (Tm) of acetic acid decreased with the increase of average separation voltage (Va), and when RNA denatured in 4.0M urea, Tm showed a linear correlation with Va. (V) The mobility of nucleic acids increased with the growth of artificial temperature in the capillary volume due to the decrease in the viscosity of the polymer. This is the first systematic and comparative research of high molecular mass nucleic acids in PFCE, which provides us deep insight into RNA and DNA migration behavior under pulsed electric field conditions. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Reversibility of partial denaturation of DNA

    International Nuclear Information System (INIS)

    Acuna, M.I.; Mingot, F.; Davila, C.A.


    The recovery of hypochromicity in a partially denatured DNA sample when salt concentration is suddenly increased at a intermediate stage of the thermal transition is studied. The results of CsCl gradient analysis, PEG/DEX partition analysis, behaviour in a new thermal transition hydrodynamic properties and transforming ability, support the view that the process is an intramolecular double chain denaturation. The degree of denaturation irreversibility is dependent on single chain molecular weight of DNA (discontinuities denisty) and upon the helicity value at which salt concentration jump is performed. Both dependences are formally interpreted according to Elton's model for base distribution in DNA. Kinetically the process behaves as being an hydrodynamically limited rewinding. (author)

  3. Screening for Amyloid Aggregation by Semi-Denaturing Detergent-Agarose Gel Electrophoresis


    Halfmann, Randal; Lindquist, Susan


    Amyloid aggregation is associated with numerous protein misfolding pathologies and underlies the infectious properties of prions, which are conformationally self-templating proteins that are thought to have beneficial roles in lower organisms. Amyloids have been notoriously difficult to study due to their insolubility and structural heterogeneity. However, resolution of amyloid polymers based on size and detergent insolubility has been made possible by Semi-Denaturing Detergent-Agarose Gel El...

  4. Corneal collagen denaturation in laser thermokeratoplasty (United States)

    Brinkmann, Ralf; Kampmeier, Juergen; Grotehusmann, Ulf; Vogel, Alfred; Koop, Norbert; Asiyo-Vogel, Mary; Birngruber, Reginald


    In laserthermokeratoplasty (LTK) thermal denaturation and shrinkage of corneal collagen is used to correct hyperopia and astigmatism. In order to optimize dosimetry, the temperature at which maximal shrinkage of collagen fibrils occurs is of major interest. Since the exposure time in clinical LTK-treatment is limited to a few seconds, the kinetics of collagen denaturation as a rate process has to be considered, thus the time of exposure is of critical importance for threshold and shrinkage temperatures. We investigated the time-temperature correlation for corneal collagen denaturation within different time domains by turbidimetry of scattered HeNe laser probe light using a temperature controlled water bath and pulsed IR laser irradiation. In the temperature range of 60 degree(s)C to 95 degree(s)C we found an exponential relation between the denaturation time and temperature. For the typical LTK-treatment time of 2 s, a temperature of 95 degree(s)C is needed to induce thermal damage. Use of pulsed Holmium laser radiation gave significant scattering of HeNe laser probe light at calculated temperatures of around 100 degree(s)DC. Rate parameters according to the formalism of Arrhenius were fitted to these results. Force measurements showed the simultaneous onset of light scattering and collagen shrinkage.

  5. Nitrous acid reactivation of ultraviolet-irradiated denatured transforming DNA

    International Nuclear Information System (INIS)

    Cabrera-Juarez, E.; Gonzalez-Dadda, L.


    Partial recovery of ultraviolet-damaged denatured transforming DNA from Haemophilus influenzae, was obtained by exposing irradiated denatured DNA to nitrous acid and assaying transforming activity. This reactivation was affected by the time of incubation with nitrous acid. (author)

  6. Guanidinium-induced denaturation by breaking of salt bridges

    NARCIS (Netherlands)

    Meuzelaar, H.; Panman, M.R.; Woutersen, S.


    Despite its wide use as a denaturant, the mechanism by which guanidinium (Gdm+) induces protein unfolding remains largely unclear. Herein, we show evidence that Gdm+ can induce denaturation by disrupting salt bridges that stabilize the folded conformation. We study the Gdm+-​induced denaturation of

  7. Hysteresis in pressure-driven DNA denaturation.

    Directory of Open Access Journals (Sweden)

    Enrique Hernández-Lemus

    Full Text Available In the past, a great deal of attention has been drawn to thermal driven denaturation processes. In recent years, however, the discovery of stress-induced denaturation, observed at the one-molecule level, has revealed new insights into the complex phenomena involved in the thermo-mechanics of DNA function. Understanding the effect of local pressure variations in DNA stability is thus an appealing topic. Such processes as cellular stress, dehydration, and changes in the ionic strength of the medium could explain local pressure changes that will affect the molecular mechanics of DNA and hence its stability. In this work, a theory that accounts for hysteresis in pressure-driven DNA denaturation is proposed. We here combine an irreversible thermodynamic approach with an equation of state based on the Poisson-Boltzmann cell model. The latter one provides a good description of the osmotic pressure over a wide range of DNA concentrations. The resulting theoretical framework predicts, in general, the process of denaturation and, in particular, hysteresis curves for a DNA sequence in terms of system parameters such as salt concentration, density of DNA molecules and temperature in addition to structural and configurational states of DNA. Furthermore, this formalism can be naturally extended to more complex situations, for example, in cases where the host medium is made up of asymmetric salts or in the description of the (helical-like charge distribution along the DNA molecule. Moreover, since this study incorporates the effect of pressure through a thermodynamic analysis, much of what is known from temperature-driven experiments will shed light on the pressure-induced melting issue.

  8. Denaturing urea polyacrylamide gel electrophoresis (Urea PAGE). (United States)

    Summer, Heike; Grämer, René; Dröge, Peter


    Urea PAGE or denaturing urea polyacrylamide gel electrophoresis employs 6-8 M urea, which denatures secondary DNA or RNA structures and is used for their separation in a polyacrylamide gel matrix based on the molecular weight. Fragments between 2 to 500 bases, with length differences as small as a single nucleotide, can be separated using this method(1). The migration of the sample is dependent on the chosen acrylamide concentration. A higher percentage of polyacrylamide resolves lower molecular weight fragments. The combination of urea and temperatures of 45-55 degrees C during the gel run allows for the separation of unstructured DNA or RNA molecules. In general this method is required to analyze or purify single stranded DNA or RNA fragments, such as synthesized or labeled oligonucleotides or products from enzymatic cleavage reactions. In this video article we show how to prepare and run the denaturing urea polyacrylamide gels. Technical tips are included, in addition to the original protocol (1,2).

  9. Characterization of denaturation and renaturation of DNA for DNA hybridization

    Directory of Open Access Journals (Sweden)

    Xiaofang Wang


    Full Text Available Objectives The present study was designed to systematically characterize the denaturation and the renaturation of double stranded DNA (dsDNA, which is suitable for DNA hybridization. Methods A series of physical and chemical denaturation methods were implemented on well-defined 86-bp dsDNA fragment. The degree of each denaturation was measured and the most suitable denaturation method was determined. DNA renaturation tendency was also investigated for the suggested denaturation method. Results Heating, beads mill, and sonication bath did not show any denaturation for 30 minutes. However probe sonication fully denatured DNA in 5 minutes. 1 mol/L sodium hydroxide (alkaline treatment and 60% dimethyl sulfoxide (DMSO treatment fully denatured DNA in 2-5 minutes. Conclusions Among all the physical methods applied, the direct probe sonication was the most effective way to denature the DNA fragments. Among chemical methods, 60% DMSO was the most adequate denaturation method since it does not cause full renaturation during DNA hybridization.

  10. Hemichrome formation during hemoglobin Zurich denaturation

    International Nuclear Information System (INIS)

    Zago, M.A.; Costa, F.F.; Botura, C.; Baffa, O.


    Electron paramagnetic resonance (EPR)spectrum of hemoglobin Zurich, after oxidation, storage and heating, showed several absorption derives in the high field region (g ≅ 2) which are indicative of hemichrome formation. Characteristic visible spectra of hemichromes were observed for oxidized Hb Zurich and for its spontaneous precipitate. The proportional increase of EPR signals at g ≅ 2 and decrease at g = 6.37, the constant ratio of absorbance at 540 nm to 280 nm during heating, and the similarity of this ratio for spontaneously precipitated HbA and for Hb Zurich indicate that heme is not lost during the first steps of Hb Zurich denaturation. (author) [pt

  11. 78 FR 38628 - Reclassification of Specially Denatured Spirits and Completely Denatured Alcohol Formulas and... (United States)


    ... generally determined at the time the distilled spirits are withdrawn from the bonded premises of a distilled... industry, or for fuel, light, or power, except that, under 26 U.S.C. 5273(b), denatured spirits may not be....D.S.'' for purposes of this preamble). C.D.A. jeopardizes the revenue less than S.D.S. does--first...

  12. 27 CFR 21.151 - List of denaturants authorized for denatured spirits. (United States)



  13. Partially folded intermediates during trypsinogen denaturation

    Directory of Open Access Journals (Sweden)

    Martins N.F.


    Full Text Available The equilibrium unfolding of bovine trypsinogen was studied by circular dichroism, differential spectra and size exclusion HPLC. The change in free energy of denaturation was = 6.99 ± 1.40 kcal/mol for guanidine hydrochloride and = 6.37 ± 0.57 kcal/mol for urea. Satisfactory fits of equilibrium unfolding transitions required a three-state model involving an intermediate in addition to the native and unfolded forms. Size exclusion HPLC allowed the detection of an intermediate population of trypsinogen whose Stokes radii varied from 24.1 ± 0.4 Å to 26.0 ± 0.3 Å for 1.5 M and 2.5 M guanidine hydrochloride, respectively. During urea denaturation, the range of Stokes radii varied from 23.9 ± 0.3 Å to 25.7 ± 0.6 Å for 4.0 M and 6.0 M urea, respectively. Maximal intrinsic fluorescence was observed at about 3.8 M urea with 8-aniline-1-naphthalene sulfonate (ANS binding. These experimental data indicate that the unfolding of bovine trypsinogen is not a simple transition and suggest that the equilibrium intermediate population comprises one intermediate that may be characterized as a molten globule. To obtain further insight by studying intermediates representing different stages of unfolding, we hope to gain a better understanding of the complex interrelations between protein conformation and energetics.

  14. The Denaturation Transition of DNA in Mixed Solvents (United States)

    Hammouda, Boualem; Worcester, David


    The helix-to-coil denaturation transition in DNA has been investigated in mixed solvents at high concentration using ultraviolet light absorption spectroscopy and small-angle neutron scattering. Two solvents have been used: water and ethylene glycol. The “melting” transition temperature was found to be 94°C for 4% mass fraction DNA/d-water and 38°C for 4% mass fraction DNA/d-ethylene glycol. The DNA melting transition temperature was found to vary linearly with the solvent fraction in the mixed solvents case. Deuterated solvents (d-water and d-ethylene glycol) were used to enhance the small-angle neutron scattering signal and 0.1M NaCl (or 0.0058 g/g mass fraction) salt concentration was added to screen charge interactions in all cases. DNA structural information was obtained by small-angle neutron scattering, including a correlation length characteristic of the inter-distance between the hydrogen-containing (desoxyribose sugar-amine base) groups. This correlation length was found to increase from 8.5 to 12.3 Å across the melting transition. Ethylene glycol and water mixed solvents were found to mix randomly in the solvation region in the helix phase, but nonideal solvent mixing was found in the melted coil phase. In the coil phase, solvent mixtures are more effective solvating agents than either of the individual solvents. Once melted, DNA coils behave like swollen water-soluble synthetic polymer chains. PMID:16815902

  15. Study of polymer molecules and conformations with a nanopore

    Energy Technology Data Exchange (ETDEWEB)

    Golovchenko, Jene A; Li, Jiali; Stein, Derek; Gershow, Marc H


    The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

  16. Study of polymer molecules and conformations with a nanopore (United States)

    Golovchenko, Jene A.; Li, Jiali; Stein, Derek; Gershow, Marc H.


    The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

  17. Study of polymer molecules and conformations with a nanopore (United States)

    Golovchenko, Jene A.; Li, Jiali; Stein, Derek; Gershow, Marc H.


    The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

  18. Simulated pressure denaturation thermodynamics of ubiquitin. (United States)

    Ploetz, Elizabeth A; Smith, Paul E


    Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Reversible thermal denaturation of immobilized rhodanese

    International Nuclear Information System (INIS)

    Horowitz, P.; Bowman, S.


    For the first time, the enzyme rhodanese had been refolded after thermal denaturation. This was previously not possible because of the strong tendency for the soluble enzyme to aggregate at temperatures above 37 degrees C. The present work used rhodanese that was covalently coupled to a solid support under conditions that were found to preserve enzyme activity. Rhodanese was immobilized using an N-hydroxymalonimidyl derivative of Sepharose containing a 6-carbon spacer. The number of immobilized competent active sites was measured by using [ 35 S]SO 3 (2-) to form an active site persulfide that is the obligatory catalytic intermediate. Soluble enzyme was irreversibly inactivated in 10 min at 52 degrees C. The immobilized enzyme regained at least 30% of its original activity even after boiling for 20 min. The immobilized enzyme had a Km and Vmax that were each approximately 3 times higher than the corresponding values for the native enzyme. After preincubation at high temperatures, progress curves for the immobilized enzyme showed induction periods of up to 5 min before attaining apparently linear steady states. The pH dependence of the activity was the same for both the soluble and the immobilized enzyme. These results indicate significant stabilization of rhodanese after immobilization, and instabilities caused by adventitious solution components are not the sole reasons for irreversibility of thermal denaturation seen with the soluble enzyme. The results are consistent with models for rhodanese that invoke protein association as a major cause of inactivation of the enzyme. Furthermore, the induction period in the progress curves is consistent with studies which show that rhodanese refolding proceeds through intermediate states

  20. Single-molecule denaturation mapping of DNA in nanofluidic channels

    DEFF Research Database (Denmark)

    Reisner, Walter; Larsen, Niels Bent; Silahtaroglu, Asli


    Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO (R)-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips...

  1. Statistical mechanics of thermal denaturation of DNA oligomers

    Indian Academy of Sciences (India)

    Double stranded DNA chain is known to have non-trivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been ...

  2. 27 CFR 20.261 - Records of completely denatured alcohol. (United States)


    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Records of completely denatured alcohol. 20.261 Section 20.261 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DISTRIBUTION AND USE OF DENATURED ALCOHOL AND RUM...

  3. 27 CFR 20.144 - Packages of completely denatured alcohol. (United States)


    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Packages of completely denatured alcohol. 20.144 Section 20.144 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DISTRIBUTION AND USE OF DENATURED ALCOHOL AND RUM Sale...

  4. Guanidinium-Induced Denaturation by Breaking of Salt Bridges. (United States)

    Meuzelaar, Heleen; Panman, Matthijs R; Woutersen, Sander


    Despite its wide use as a denaturant, the mechanism by which guanidinium (Gdm(+) ) induces protein unfolding remains largely unclear. Herein, we show evidence that Gdm(+) can induce denaturation by disrupting salt bridges that stabilize the folded conformation. We study the Gdm(+) -induced denaturation of a series of peptides containing Arg/Glu and Lys/Glu salt bridges that either stabilize or destabilize the folded conformation. The peptides containing stabilizing salt bridges are found to be denatured much more efficiently by Gdm(+) than the peptides containing destabilizing salt bridges. Complementary 2D-infrared measurements suggest a denaturation mechanism in which Gdm(+) binds to side-chain carboxylate groups involved in salt bridges. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Guide to electrospinning denatured whole chain collagen from hoki fish using benign solvents. (United States)

    Le Corre-Bordes, Deborah; Hofman, Kathleen; Hall, Bronwyn


    Tissue engineering requires the design and manufacture of biomimetic scaffolds. Collagen-derived nanofibrous scaffolds have been intensively studied because collagen, in the form of fibrils, is one of the main components of the extra cellular matrix (ECM). Several collagen materials have been used in electrospinning studies including mammalian extracted Type I collagen and gelatin formulations. Denatured whole chain collagen (DWCC) can be prepared by heat denaturing acid-soluble collagen extracted from cold-water fish skin. This product provides a consistent source of collagen with a controlled molecular weight profile and intact alpha chains including telopeptides. In this work, we studied DWCC-water-acid systems in order to determine the effect of solution composition on nanofibre morphology. Whereas measurement of the classical physical properties of concentrated solutions failed to predict and only partially explained the electrospinning behavior of collagen derived polymers, hydrodynamic properties provided insight. All the samples are presented in ternary diagrams to map the electrospinnability of the systems. These "electrospinning maps" provide an informative resource to electrospinning collagen-derived product for biomedical or commercial applications and a practical alternative to complicated models developed for synthetic polymers. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. Affective identities: Denaturalization and the politics of nationality in France

    NARCIS (Netherlands)

    Beauchamps, M.L.


    This dissertation investigates denaturalization (i.e. the deprivation of citizenship). The context is the politics of citizenship and nationality in France. Combining research insights from history, legal studies, security studies, and narratology, it demonstrates that the language of

  7. Light water reactors with a denatured thorium fuel cycle

    International Nuclear Information System (INIS)


    Discussed in this paper is the performance of denatured thorium fuel cycles in PWR plants of conventional design, such as those currently in operation or under construction. Although some improvement in U 3 O 8 utilization is anticipated in PWRs optimized explicitly for the denatured thorium fuel cycle, this paper is limited to a discussion of the performance of denatured thorium fuels in conventional PWRs and consequently the data presented is representative of the use of thorium fuel in existing PWRs or those presently under construction. In subsequent sections of this paper, the design of the PWR, its performance on the denatured thorium fuel cycle, safety, accident and environmental considerations, and technological status and R and D requirements are discussed

  8. Purification of radiolabeled RNA products using denaturing gel electrophoresis


    Adachi, Hironori; Yu, Yi-Tao


    This unit discusses a basic method for purification of radiolabeled RNAs using denaturing polyacrylamide gel electrophoresis. The method consists of a number of experimental procedures, including total RNA preparation from yeast cells, isolation of a specific RNA from total yeast RNA, RNA 3' terminal labeling using nucleotide (5’[32P]pCp) addition (via ligation), denaturing (8 M urea) polyacrylamide gel electrophoresis, and RNA extraction from the gel slice. Key points for achieving good elec...

  9. The fabrication and modification of capillary polymer monoliths for the separation of small ions


    Moyna, Aine


    The fabrication and modification of polymer monoliths, in capillary formats, for the separation of small ions is presented. The separation of small ions using polymer monoliths has limitations and this work aims to investigate increasing the ion exchange capacity using photo-grafting techniques. Chapter 1.0 includes a comprehensive review on the use of capillary ion chromatography including advancements made in capillary instrumentation, stationary phases and detection devices. This chapter a...

  10. Cold denaturation of α-synuclein amyloid fibrils. (United States)

    Ikenoue, Tatsuya; Lee, Young-Ho; Kardos, József; Saiki, Miyu; Yagi, Hisashi; Kawata, Yasushi; Goto, Yuji


    Although amyloid fibrils are associated with numerous pathologies, their conformational stability remains largely unclear. Herein, we probe the thermal stability of various amyloid fibrils. α-Synuclein fibrils cold-denatured to monomers at 0-20 °C and heat-denatured at 60-110 °C. Meanwhile, the fibrils of β2-microglobulin, Alzheimer's Aβ1-40/Aβ1-42 peptides, and insulin exhibited only heat denaturation, although they showed a decrease in stability at low temperature. A comparison of structural parameters with positive enthalpy and heat capacity changes which showed opposite signs to protein folding suggested that the burial of charged residues in fibril cores contributed to the cold denaturation of α-synuclein fibrils. We propose that although cold-denaturation is common to both native proteins and misfolded fibrillar states, the main-chain dominated amyloid structures may explain amyloid-specific cold denaturation arising from the unfavorable burial of charged side-chains in fibril cores. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Thermal denaturation of type I collagen vitrified gels

    International Nuclear Information System (INIS)

    Xia, Zhiyong; Calderon-Colon, Xiomara; Trexler, Morgana; Elisseeff, Jennifer; Guo, Qiongyu


    Highlights: ► We analyzed the denaturation of vitrigels synthesized under different conditions. ► Overall denaturation kinetics consisted of both reversible and irreversible steps. ► More stable vitrigels were formed under high level of vitrification. - Abstract: The denaturation kinetics of type I collagen vitrigels synthesized under different vitrification time and temperature were analyzed by the classical Kissinger approach and the advanced model free kinetics (AMFK) using the Vyazovkin algorithm. The AMFK successfully elucidated the overall denaturation into reversible and irreversible processes. Depending on vitrification conditions, the activation energy for the irreversible process ranged from 100 to 200 kJ/mol, and the reversible enthalpy ranged from 250 to 300 kJ/mol. All of these values increased with the vitrification time and temperature, indicating that a more stable and complex structure formed with increased vitrification. The classical Kissinger method predicted the presence of a critical temperate of approximately 60 °C for the transition between reversible and irreversible processes. Scanning electron microscopy revealed the presence of fibril structures in vitrigels both before and after full denaturation; however the fibrils had became thicker and rougher after denaturation.

  12. 27 CFR 28.310 - Loss of specially denatured spirits in transit. (United States)


    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Loss of specially denatured spirits in transit. 28.310 Section 28.310 Alcohol, Tobacco Products and Firearms ALCOHOL AND... Denatured Spirits § 28.310 Loss of specially denatured spirits in transit. Losses of specially denatured...

  13. On the mobility of partially denatured DNA in gel electrophoresis: a theoretical investigation (United States)

    Sean, David

    There are technologies which exploit a rapid reduction of the gel electrophoretic mobility of DNA arising from partial denaturation. The underlying phenomenon behind these experiments---the mechanisms which reduce the mobility---are not very well understood. Such is the purpose of my thesis. The first chapter provides a brief introduction to the field of polymer physics. The subjects covered are carefully chosen to directly relate to the forthcoming research. There is a published semi-empirical formula used to model the rapid decrease of mobility which is largely considered to be consistent with experimental data. The second chapter of this thesis demonstrates that there is a fundamental confusion in the literature regarding the fitting parameter Lr, in the said formula. By going back to the original derivation, a physical interpretation can be given to L r. This interpretation yields theoretical values which are consistent with what has been published. However, we find that an underlying assumption---that the effect of the denaturation does not depend on its position along the DNA fragment---may systematically overestimate experimental observations of Lr. To measure the impact of this assumption, a simulation model of DNA is presented. The article presented in the third chapter reveals that indeed, the position of the denatured region affects the migration of the DNA fragment. A refined version of the formula which takes these factors into account is proposed. The simulations also reveal that, for certain fields, an unexpected conformation completely dominates during migration of the fragment. This surprising result: a squid-like conformation, is explored in chapter four.

  14. Capture of microparticles by bolus flow in capillaries (United States)

    Takeishi, Naoki; Imai, Yohsuke; BFSL Collaboration


    Previous studies have concluded that microparticles (MPs) can more effectively approach the microvessel wall than nanoparticles because of margination. In this study, however, we show that MPs are not marginated in capillaries where the vessel diameter is comparable to that of red blood cells (RBCs). We numerically investigated the behavior of MPs with a diameter of 1 µm in various microvessel sizes, including capillaries. In capillaries, the flow mode of RBCs shifted from multi-file flow to bolus flow, and MPs were captured by the bolus flow of the RBCs instead of being marginated. Once MPs were captured, they rarely escaped from the vortex-like flow structures between RBCs. These capture events were enhanced when the hematocrit was decreased, and reduced when the shear rate was increased. Our results suggest that microparticles may be rather inefficient drug carriers when targeting capillaries because of capture events, but nanoparticles, which are more randomly distributed in capillaries, may be more effective carriers. This research was supported by JSPS KAKENHI Grant Numbers 25000008 and 16J11479.

  15. Effects of reduction on the denaturation kinetics of human hair. (United States)

    Wortmann, F-J; Popescu, C; Sendelbach, G


    Although human hair as an alpha-keratinous fiber exhibits a complex morphology, it can be considered as a nano-structured filament/matrix composite for the context of thermal analysis. Using differential scanning calorimetry (DSC) in water, the denaturation performance of the alpha-helical protein fraction and the effects of reductive treatments were studied. The results are viewed in the context of a previous study for oxidative treatments. It was found that the course of the denaturation process remains generally unperturbed by the treatment, following an irreversible, one-step, first-order process. Arrhenius activation energies and pre-exponential factors were determined from the DSC-curves by applying the principles of the Friedman-method. Comparing activation energy values between reductive and oxidative processes shows the differences of the effects on the components of the composite. In contrast, the values of the rate constant at the denaturation temperature, though showing differences in their trends with cumulative treatments, are very similar. This further emphasizes the theory that the viscosity of the matrix affects strict kinetic control over the denaturation of the alpha-helical segments. Once the viscosity of the matrix has decreased enough for the denaturation process to occur, this follows a path that is largely independent of the temperature range and of the chemical pre-history.

  16. "Cooperative collapse" of the denatured state revealed through Clausius-Clapeyron analysis of protein denaturation phase diagrams. (United States)

    Tischer, Alexander; Machha, Venkata R; Rösgen, Jörg; Auton, Matthew


    Protein phase diagrams have a unique potential to identify the presence of additional thermodynamic states even when non-2-state character is not readily apparent from the experimental observables used to follow protein unfolding transitions. Two-state analysis of the von Willebrand factor A3 domain has previously revealed a discrepancy in the calorimetric enthalpy obtained from thermal unfolding transitions as compared with Gibbs-Helmholtz analysis of free energies obtained from the Linear Extrapolation Method (Tischer and Auton, Prot Sci 2013; 22(9):1147-60). We resolve this thermodynamic conundrum using a Clausius-Clapeyron analysis of the urea-temperature phase diagram that defines how ΔH and the urea m-value interconvert through the slope of c m versus T, (∂cm/∂T)=ΔH/(mT). This relationship permits the calculation of ΔH at low temperature from m-values obtained through iso-thermal urea denaturation and high temperature m-values from ΔH obtained through iso-urea thermal denaturation. Application of this equation uncovers sigmoid transitions in both cooperativity parameters as temperature is increased. Such residual thermal cooperativity of ΔH and the m-value confirms the presence of an additional state which is verified to result from a cooperative phase transition between urea-expanded and thermally-compact denatured states. Comparison of the equilibria between expanded and compact denatured ensembles of disulfide-intact and carboxyamidated A3 domains reveals that introducing a single disulfide crosslink does not affect the presence of the additional denatured state. It does, however, make a small thermodynamically favorable free energy (∼-13 ± 1 kJ/mol) contribution to the cooperative denatured state collapse transition as temperature is raised and urea concentration is lowered. The thermodynamics of this "cooperative collapse" of the denatured state retain significant compensations between the enthalpy and entropy contributions to the overall

  17. Efficient renaturation of inclusion body proteins denatured by SDS. (United States)

    He, Chuan; Ohnishi, Kouhei


    Inclusion bodies are often formed when the foreign protein is over expressed in Escherichia coli. Since proteins in inclusion bodies are inactive, denaturing and refolding of inclusion body proteins are necessary to obtain the active form. Instead of the conventional denaturants, urea and guanidine hydrochloride, a strong anionic detergent SDS was used to solubilize C-terminal His-tag form of ulvan lyase in the inclusion bodies. Solution containing SDS-solubilized enzyme were kept on ice to precipitate SDS, followed by SDS-KCl insoluble crystal formation to remove SDS completely. After removing the precipitate by centrifugation, the supernatant was applied to Ni-NTA column to purify His-tagged ulvan lyase. The purified protein showed a dimeric form and ulvan lyase activity, demonstrating that SDS-denatured protein was renatured and recovered enzyme activity. This simple method could be useful for refolding other inclusion body proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Improved single-strand DNA sizing accuracy in capillary electrophoresis.


    Rosenblum, B B; Oaks, F; Menchen, S; Johnson, B


    Interpolation algorithms can be developed to size unknown single-stranded (ss) DNA fragments based on their electrophoretic mobilities, when they are compared with the mobilities of standard fragments of known sizes; however, sequence-specific anomalous electrophoretic migration can affect the accuracy and precision of the called sizes of the fragments. We used the anomalous migration of ssDNA fragments to optimize denaturation conditions for capillary electrophoresis. The capillary electroph...

  19. Purification of radiolabeled RNA products using denaturing gel electrophoresis. (United States)

    Adachi, Hironori; Yu, Yi-Tao


    This unit discusses a basic method for purification of radiolabeled RNAs using denaturing polyacrylamide gel electrophoresis. The method consists of a number of experimental procedures, including total RNA preparation from yeast cells, isolation of a specific RNA from total yeast RNA, RNA 3'-terminal labeling using nucleotide (5' [(32) P]pCp) addition (via ligation), denaturing (8 M urea) polyacrylamide gel electrophoresis, and RNA extraction from the gel slice. Key points for achieving good electrophoretic separation of RNA are also discussed. Copyright © 2014 John Wiley & Sons, Inc.

  20. Heavy water reactors on the denatured thorium cycles

    International Nuclear Information System (INIS)


    This paper presents preliminary technical and economic data to INFCE on the denatured U-233/Thorium fuel cycle for use in early comparisons of alternate nuclear systems. The once-through uranium fuel cycle is discussed in a companion paper. In presenting this preliminary information at this time, it is recognized that there are several other denatured thorium fuel cycles of potential interest, such as the U-235/thorium cycle which could be implemented at an earlier date. Information on these alternate cycles is currently being developed, and will be provided to INFCE when available

  1. The application of polymerase chain reaction-denaturing gradient ...

    African Journals Online (AJOL)

    A rapid microbial screening method was developed based on denaturing gradient gel electrophoresis (DGGE). To evaluate the repeatability and reliability of this system, three DGGE markers were used. Then, the feasibility of DGGE method was verified by microbial screenings in viili (a traditional fermented dairy product ...

  2. DNA sequencing by denaturation: principle and thermodynamic simulations. (United States)

    Chen, Ying-Ja; Huang, Xiaohua


    We describe a new DNA sequencing method called sequencing by denaturation (SBD). A Sanger dideoxy sequencing reaction is performed on the templates on a solid surface to generate a ladder of DNA fragments randomly terminated by fluorescently labeled dideoxyribonucleotides. The labeled DNA fragments are sequentially denatured from the templates and the process is monitored by measuring the change in fluorescence intensities from the surface. By analyzing the denaturation profiles, the base sequence of the template can be determined. Using thermodynamic principles, we simulated the denaturation profiles of a series of oligonucleotides ranging from 12 to 32 bases and developed a base-calling algorithm to decode the sequences. These simulations demonstrate that DNA molecules up to 20 bases can be sequenced by SBD. Experimental measurements of the melting profiles of DNA fragments in solution confirm that DNA sequences can be determined by SBD. The potential limitations and advantages of SBD are discussed. With SBD, millions of sequencing reactions can be performed on a small area on a surface in parallel with a very small amount of sequencing reagents. Therefore, DNA sequencing by SBD could potentially result in a significant increase in speed and reduction in cost in large-scale genome resequencing.

  3. Statistical mechanics of thermal denaturation of DNA oligomers

    Indian Academy of Sciences (India)

    Statistical mechanics of thermal denaturation of DNA oligomers. NAVIN SINGH and YASHWANT SINGH. Department of Physics, Banaras Hindu University, Varanasi 221 005, India. Email: Abstract. Double stranded DNA chain is known to have non-trivial elasticity. We study the effect of this elasticity on ...

  4. Cold denaturation of the HIV-1 protease monomer

    DEFF Research Database (Denmark)

    Rösner, Heike Ilona; Caldarini, Martina; Prestel, Andreas


    The HIV-1-protease is a complex protein which in its active form adopts a homodimer dominated by -sheet structures. We have discovered a cold-denatured state of the monomeric subunit of HIV-1-protease which is populated above 0ºC and therefore directly accessible to various spectroscopic...

  5. Role of cyclobutane dimers in UV-denaturation of DNA

    International Nuclear Information System (INIS)

    Zavil'gel'skij, G.B.; Zuev, A.V.


    UV irradiation of double-stranded DNA produces local denatured regions. The evidence presented indicates that these single-stranded regions arise from photoproducts other than pyrimidine dimers. The irradiation of T2 DNA at 8x10 4 erg/mm 2 (254 nm) produces 6-8% thymine dimers, amd Tsub(mel) drops by 12-14 deg C, accompanied by a significant broadening of the transition profile. The kinetics of denatured region formation and lowering Tsub(mel) corresponds to that of formation of crosslinkages and differs markedly from the kinetics of formation of cyclobutane pyrimidine dimers. Treatment of UV-irradiated DNA with light in the presence of yeast photoreactivating enzyme monomerizes almost all thymine dimers but does not change the Tsub(mel). Local denatured regions are detected in UV-irradiated DNA and are absent from AcPhM-sensibilized DNA, which contains 20-25% thymine dimers, as determined by the accridine orange fluorescence technique. S1 nuclease from Aspergillis oryzae produces single-strand breaks in UV-irradiated DNA of phage PM2 but is not active on AcPhM-treated PM2 DNA, which contains about 50 thymine dimers. It is supposed that the formation of a cyclobutane dimer only weakens the hydrogen bonds in the AT base pair rather than breaks them. Local denatured regions are thought to arise from the accumulation in UV-irradiated DNA (254 nm) of the sufficient number of photoproducts with impaired ability to base pairing

  6. Denaturation of membrane proteins and hyperthermic cell killing

    NARCIS (Netherlands)

    Burgman, Paulus Wilhelmus Johannes Jozef


    Summarizing: heat induced denaturation of membrane proteins is probably related to hyperthermic cell killing. Induced resistance of heat sensitive proteins seems to be involved in the development of thermotolerance. Although many questions remain still to be answered, it appears that HSP72, when

  7. Evaluation of denaturing gradient gel electrophoresis (DGGE) used ...

    African Journals Online (AJOL)

    Denaturing gradient gel electrophoresis (DGGE) is a powerful method used to study structure of bacterial communities, without cultivation, based on the diversity of the genes coding for ribosomal RNA. However, the results are strongly dependent on the respective target region of the used primer systems. Therefore, three ...

  8. Denaturing and non-denaturing gel electrophoresis as methods for the detection ofjunctional diversity in rearranged T cell receptor sequences

    NARCIS (Netherlands)

    Offermans, M.T.C.; Sonneveld, R.D.; Bakker, E.; Deutz-Terlouw, P.P.; Geus, B. de; Rozing, J.


    Two nucleic acid gel electrophoresis techniques were tested as a possible tool for analyzing junctional diversity in rearranged T cell receptor (TcR) sequences in order to define the extent of T cell heterogeneity. For this purpose denaturing gradient gel electrophoresis (DGGE) as well as

  9. An analytical model for enantioseparation process in capillary electrophoresis (United States)

    Ranzuglia, G. A.; Manzi, S. J.; Gomez, M. R.; Belardinelli, R. E.; Pereyra, V. D.


    An analytical model to explain the mobilities of enantiomer binary mixture in capillary electrophoresis experiment is proposed. The model consists in a set of kinetic equations describing the evolution of the populations of molecules involved in the enantioseparation process in capillary electrophoresis (CE) is proposed. These equations take into account the asymmetric driven migration of enantiomer molecules, chiral selector and the temporary diastomeric complexes, which are the products of the reversible reaction between the enantiomers and the chiral selector. The solution of these equations gives the spatial and temporal distribution of each species in the capillary, reproducing a typical signal of the electropherogram. The mobility, μ, of each specie is obtained by the position of the maximum (main peak) of their respective distributions. Thereby, the apparent electrophoretic mobility difference, Δμ, as a function of chiral selector concentration, [ C ] , can be measured. The behaviour of Δμ versus [ C ] is compared with the phenomenological model introduced by Wren and Rowe in J. Chromatography 1992, 603, 235. To test the analytical model, a capillary electrophoresis experiment for the enantiomeric separation of the (±)-chlorpheniramine β-cyclodextrin (β-CD) system is used. These data, as well as, other obtained from literature are in closed agreement with those obtained by the model. All these results are also corroborate by kinetic Monte Carlo simulation.

  10. Quantitative analysis in capillary electrophoresis: transformation of raw electropherograms into continuous distributions. (United States)

    Chamieh, Joseph; Martin, Michel; Cottet, Hervé


    Quantitative analysis in capillary electrophoresis based on time-scale electropherograms generally uses time-corrected peak areas to account for the differences in apparent velocities between solutes. However, it could be convenient and much more relevant to change the time-scale electropherograms into mass relative distribution of the effective mobility or any other characteristic parameter (molar mass, chemical composition, charge density, ...). In this study, the theoretical background required to perform the variable change on the electropherogram was developed with an emphasis on the fact that both x and y axes should be changed when the time scale electropherograms are modified to get the distributions. Applications to the characterization of polymers and copolymers by different modes of capillary electrophoresis (CE) are presented, including the molar mass distribution of poly-L-lysine oligomers by capillary gel electrophoresis (CGE), molar mass distribution of end-charged poly-l-alanine by free solution CE, molar mass distribution of evenly charged polyelectrolytes by CGE, and charge density distribution of variously charged polyelectrolytes by free solution CE.

  11. Heat denaturation of Brazil nut allergen Ber e 1 in relation to food processing

    NARCIS (Netherlands)

    Boxtel, E.L. van; Koppelman, S.J.; Broek, L.A.M. van den; Gruppen, H.


    Ber e 1, a major allergen from Brazil nuts, is very stable to in vitro peptic digestion. As heat-induced denaturation may affect protein digestibility, the denaturation behaviour of Ber e 1 was investigated. The denaturation temperature of Ber e 1 varies from approximately 80-110 °C, depending on

  12. Spectral shift controlled reactors, denatured U-233/thorium cycle

    International Nuclear Information System (INIS)


    This paper presents technical and economic data on the SSCR which may be of use in the International Fuel Cycle Evaluation Program to intercompare alternative nuclear systems. Included in this paper are data on the denatured U-233/thorium cycle. This cycle shows a proliferation advantage over more classical thorium fuel cycle (e.g., highly-enriched U-235/thorium or plutonium/thorium) due to the elimination of chemically-separable, concentrated fissile material from unirradiated nuclear fuel. The U-233 is denatured by mixing with depleted uranium to a concentration no greater than 12 w/o. An exogenous source of U-233 is assumed in this paper, since U-233 does not occur in nature and only a limited supply has been produced to date for research and development work

  13. Preparation of denatured protein bone sterilized with gamma radiation

    International Nuclear Information System (INIS)

    Luna Z, D.


    The bone is one of the tissues more transplanted in the entire world by that the bone necessity for transplant every day becomes bigger. In the Bank of tissues Radio sterilized of the ININ the amnion and the pig skin are routinely processed. The tissue with which will be continued is with bone. Due to that in our country it doesn't have enough bone of human origin for the necessities required in the bone transplant, an option is the bone of bovine. Of this bone one can obtain denatured protein bone, with the same characteristics of the denatured protein human bone, the one which has been proven that it has good acceptance and incorporation in the human body when is transplanted. The method for the obtaining of the denatured protein bone of bovine, with the confirmation of the final product by means of X-ray diffraction is described. The radiosterilization of this bone with gamma rays and the determination of the lead content. (Author)

  14. Polymer films (United States)

    Granick, Steve; Sukhishvili, Svetlana A.


    A film contains a first polymer having a plurality of hydrogen bond donating moieties, and a second polymer having a plurality of hydrogen bond accepting moieties. The second polymer is hydrogen bonded to the first polymer.

  15. Bioinspired phospholipid polymer biomaterials for making high performance artificial organs

    Directory of Open Access Journals (Sweden)

    K Ishihara


    Full Text Available Novel polymer biomaterials, which can be used in contact with blood, are prepared with strong inspiration from the surface structure of biomembrane. That is, the polymers with a phospholipid polar group in the side chain, 2-methacrylooyloxyethyl phosphorylcholine (MPC polymers were synthesized. The MPC polymers can inhibit surface-induced clot formation effectively, when they are in contact with blood even in the absence of an anticoagulant. This phenomenon was due to the reduction of plasma protein and suppression of denaturation of adsorbed proteins, that is the MPC polymers interact with blood components very mildly. As the molecular structure of the MPC polymer was easily designed by changing the monomer units and their composition, it could be applied to surface modification of artificial organs and biomedical devices for improving blood and tissue compatibility. Thus, the MPC polymers are useful polymer biomaterials for manufacturing high performance artificial organs and biomedical devices to provide safe medical treatments.

  16. Denatured ethanol release into gasoline residuals, Part 1: Source behaviour (United States)

    Freitas, Juliana G.; Barker, James F.


    With the increasing use of ethanol in fuels, it is important to evaluate its fate when released into the environment. While ethanol is less toxic than other organic compounds present in fuels, one of the concerns is the impact ethanol might have on the fate of gasoline hydrocarbons in groundwater. One possible concern is the spill of denatured ethanol (E95: ethanol containing 5% denaturants, usually hydrocarbons) in sites with pre-existing gasoline contamination. In that scenario, ethanol is expected to increase the mobility of the NAPL phase by acting as a cosolvent and decreasing interfacial tension. To evaluate the E95 behaviour and its impacts on pre-existing gasoline, a field test was performed at the CFB-Borden aquifer. Initially gasoline contamination was created releasing 200 L of E10 (gasoline with 10% ethanol) into the unsaturated zone. One year later, 184 L of E95 was released on top of the gasoline contamination. The site was monitored using soil cores, multilevel wells and one glass access tube. At the end of the test, the source zone was excavated and the compounds remaining were quantified. E95 ethanol accumulated and remained within the capillary fringe and unsaturated zone for more than 200 days, despite ~ 1 m oscillations in the water table. The gasoline mobility increased and it was redistributed in the source zone. Gasoline NAPL saturations in the soil increased two fold in the source zone. However, water table oscillations caused a separation between the NAPL and ethanol: NAPL was smeared and remained in deeper positions while ethanol moved upwards following the water table rise. Similarly, the E95 denaturants that initially were within the ethanol-rich phase became separated from ethanol after the water table oscillation, remaining below the ethanol rich zone. The separation between ethanol and hydrocarbons in the source after water table oscillation indicates that ethanol's impact on hydrocarbon residuals is likely limited to early times.

  17. Strategies for denaturing the weapons-grade plutonium stockpile

    International Nuclear Information System (INIS)

    Buckner, M.R.; Parks, P.B.


    In the next few years, approximately 50 metric tons of weapons-grade plutonium and 150 metric tons of highly-enriched uranium (HEU) may be removed from nuclear weapons in the US and declared excess. These materials represent a significant energy resource that could substantially contribute to our national energy requirements. HEU can be used as fuel in naval reactors, or diluted with depleted uranium for use as fuel in commercial reactors. This paper proposes to use the weapons-grade plutonium as fuel in light water reactors. The first such reactor would demonstrate the dual objectives of producing electrical power and denaturing the plutonium to prevent use in nuclear weapons

  18. Potential-dependent surface denaturation of BSA in acid media

    Czech Academy of Sciences Publication Activity Database

    Paleček, Emil; Ostatná, Veronika


    Roč. 134, č. 10 (2009), s. 2076-2080 ISSN 0003-2654 R&D Projects: GA ČR(CZ) GA301/07/0490; GA ČR(CZ) GP202/07/P497; GA AV ČR(CZ) KJB100040901; GA MŠk(CZ) LC06035 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : bovine serum albumin denaturation * chronopotentiometry of BSA Subject RIV: BO - Biophysics Impact factor: 3.272, year: 2009

  19. Success and failure with phthalate buffers in capillary zone electrophoresis. (United States)

    Bocek, P; Gebauer, P; Beckers, J L


    Phthalate buffers are currently used in capillary electrophoresis as robust electrolyte systems for indirect detection. This contribution demonstrates that these buffers show regularly not only successful regions of mobilities of analytes (sample window) but also regions of failure where the migration of analytes is strongly deteriorated due to the presence of a system zone. System zones in phthalate buffers may be easily detected by UV detection and manifest themselves as peaks or dips. Peak shape diagrams are advantageously used for the prediction of the migration behavior of system zones in phthalate background electrolyte (BGE) systems at various pH. It is shown that the mobility of the system zone varies strongly with pH, is practically zero at pH values below 4 and above 7, and shows a maximum at pH 5. Thus, the system peak may coincide either with the peaks of various analytes or with the electroosmotic flow (EOF) peak. Experiments are given showing the effects of such coincidences as, e.g., zigzag detection patterns, double EOF peaks, and/or unusually broad peaks/dips. The message of this contribution is to show how to understand the electrophoretic properties of phthalate BGEs that, regardless of possible failure regions, may be successfully used in the analytical practice of capillary zone electrophoresis (CZE).

  20. Advances in capillary electrophoresis and the implications for drug discovery. (United States)

    Ouimet, Claire M; D'amico, Cara I; Kennedy, Robert T


    Many screening platforms are prone to assay interferences that can be avoided by directly measuring the target or enzymatic product. Capillary electrophoresis (CE) and microchip electrophoresis (MCE) have been applied in a variety of formats to drug discovery. CE provides direct detection of the product allowing for the identification of some forms of assay interference. The high efficiency, rapid separations, and low volume requirements make CE amenable to drug discovery. Areas covered: This article describes advances in capillary electrophoresis throughput, sample introduction, and target assays as they pertain to drug discovery and screening. Instrumental advances discussed include integrated droplet microfluidics platforms and multiplexed arrays. Applications of CE to assays of diverse drug discovery targets, including enzymes and affinity interactions are also described. Expert opinion: Current screening with CE does not fully take advantage of the throughputs or low sample volumes possible with CE and is most suitable as a secondary screening method or for screens that are inaccessible with more common platforms. With further development, droplet microfluidics coupled to MCE could take advantage of the low sample requirements by performing assays on the nanoliter scale at high throughput.

  1. Wall modified photonic crystal fibre capillaries as porous layer open tubular columns for in-capillary micro-extraction and capillary chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Kazarian, Artaches A. [Australian Centre for Research on Separation Science, School of Physical Sciences, University of Tasmania, Private Bag 75, Hobart, Tasmania 7001 (Australia); W.M. Keck FT-ICR-MS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC (United States); Sanz Rodriguez, Estrella; Deverell, Jeremy A. [Australian Centre for Research on Separation Science, School of Physical Sciences, University of Tasmania, Private Bag 75, Hobart, Tasmania 7001 (Australia); McCord, James; Muddiman, David C. [W.M. Keck FT-ICR-MS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC (United States); Paull, Brett, E-mail: [Australian Centre for Research on Separation Science, School of Physical Sciences, University of Tasmania, Private Bag 75, Hobart, Tasmania 7001 (Australia); ARC Centre of Excellence for Electromaterials Science, School of Physical Sciences, University of Tasmania, Private Bag 75, Hobart, Tasmania 7001 (Australia)


    Wall modified photonic crystal fibre capillary columns for in-capillary micro-extraction and liquid chromatographic separations is presented. Columns contained 126 internal parallel 4 μm channels, each containing a wall bonded porous monolithic type polystyrene-divinylbenzene layer in open tubular column format (PLOT). Modification longitudinal homogeneity was monitored using scanning contactless conductivity detection and scanning electron microscopy. The multichannel open tubular capillary column showed channel diameter and polymer layer consistency of 4.2 ± 0.1 μm and 0.26 ± 0.02 μm respectively, and modification of 100% of the parallel channels with the monolithic polymer. The modified multi-channel capillaries were applied to the in-capillary micro-extraction of water samples. 500 μL of water samples containing single μg L{sup −1} levels of polyaromatic hydrocarbons were extracted at a flow rate of 10 μL min{sup −1}, and eluted in 50 μL of acetonitrile for analysis using HPLC with fluorescence detection. HPLC LODs were 0.08, 0.02 and 0.05 μg L{sup −1} for acenaphthene, anthracene and pyrene, respectively, with extraction recoveries of between 77 and 103%. The modified capillaries were also investigated briefly for direct application to liquid chromatographic separations, with the retention and elution of a standard protein (cytochrome c) under isocratic conditions demonstrated, proving chromatographic potential of the new column format, with run-to-run retention time reproducibility of below 1%. - Highlights: • Novel PS-DVB modified photonic crystal fibres for in-capillary micro-extraction. • New method for micro-extraction of PAHs and HPLC-FL detection at sub-ppb levels. • Demonstration of PS-DVB modified photonic crystal fibres for capillary bioseparations.

  2. Incorporation of guanosine gels into sieving matrices for length- and sequence-based separation of DNA in capillary electrophoresis. (United States)

    Dong, Yingying; McGown, Linda B


    Sieving gels are used in capillary gel electrophoresis to resolve DNA strands of different lengths. For complex samples, however, such as those encountered in metagenomic analysis of microbial communities or biofilms, length-based separation may mask the true genetic diversity of the community since different organisms may contribute same-length DNA with different sequences. There is a need, therefore, for DNA separations based on both the length and sequence. Previous work has demonstrated the ability of guanosine gels (G-gels) to separate four single-stranded DNA 76-mers that differ by only a few A/G base substitutions. The goal of the present work is to determine whether G-gels could be combined with commercial sieving gels in order to simultaneously separate DNA based on both length and sequence. The results are given for the four 76-mers and for a standard dsDNA ladder. Commercial sieving gels were used alone and in combination with G-gels. For the 76-mers, the combined medium was less efficient than the G-gel alone but was able to achieve partial resolution. The combined medium was at least as effective as the sieving gel alone at resolving the denatured DNA ladder and showed indications of sequence-based resolution as well, as supported by MALDI-MS. The results show that the combined sieving gel/G-gel medium retains the selectivity of the individual media, providing a promising approach to simultaneous length- and sequence-based DNA separation for metagenomic analysis of complex systems. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Heterogeneity of mitochondrial DNA from Saccharomyces carlsbergensis. Denaturation mapping by electron microscopy.

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Christiansen, C; Bak, AL


    Electronmicroscopic observation of the denaturation pattern of 130 partially denaturated linear mitochondrial DNA molecules from Saccharomyces carlsbergensis was used to investigate the distribution of AT-rich sequences within the mitochondrial genome. The molecules were observed after heating...... denaturated sequences in the mitochondrial DNA. These sequences which presumably correspond to the very AT-rich regions, known to exist in the yeast mitochondrial DNA, were found at intervals of about 0.5 - 3 mum on the map....

  4. Screening for amyloid aggregation by Semi-Denaturing Detergent-Agarose Gel Electrophoresis. (United States)

    Halfmann, Randal; Lindquist, Susan


    Amyloid aggregation is associated with numerous protein misfolding pathologies and underlies the infectious properties of prions, which are conformationally self-templating proteins that are thought to have beneficial roles in lower organisms. Amyloids have been notoriously difficult to study due to their insolubility and structural heterogeneity. However, resolution of amyloid polymers based on size and detergent insolubility has been made possible by Semi-Denaturing Detergent-Agarose Gel Electrophoresis (SDD-AGE). This technique is finding widespread use for the detection and characterization of amyloid conformational variants. Here, we demonstrate an adaptation of this technique that facilitates its use in large-scale applications, such as screens for novel prions and other amyloidogenic proteins. The new SDD-AGE method uses capillary transfer for greater reliability and ease of use, and allows any sized gel to be accomodated. Thus, a large number of samples, prepared from cells or purified proteins, can be processed simultaneously for the presence of SDS-insoluble conformers of tagged proteins.

  5. Electrochemical behaviour of denatured ethanol for use in direct ethanol fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Bayer, Domnik; Kintzel, Birgit; Joos, Martin; Cremers, Carsten; Tuebke, Jens [Fraunhofer-Institut fuer Chemische Technologie (ICT), Pfinztal (Germany)


    In the present study, two denaturing agents, an adjuvant to a denaturing agent and a mixture of a denaturing agend and the adjuvant were tested with regard to their fuel cell compatibility. Therefore, various electrochemical tests including cyclic voltammetry, chronoamperometry and differential electrochemical mass spectroscopy have been conducted at platinum as model catalyst in acidic and alkaline medium. In addition, the most promising denaturing agent, a mixture of tert-butyl ethyl ether (ETBE) with the adjuvant Bitrex {sup registered}, has also been tested at commercial fuel cell catalysts in both acidic and alkaline media. (orig.)

  6. Is pulsed electric field still effective for RNA separation in capillary electrophoresis? (United States)

    Li, Zhenqing; Dou, Xiaoming; Ni, Yi; Chen, Qinmiao; Cheng, Shuyi; Yamaguchi, Yoshinori


    Pulsed field capillary electrophoresis (PFCE) is a predominant technique to cope with difficulties in resolving large DNA strands, yet it is still unclear whether pulsed electric field is effective for the separation of higher mass RNA. In this paper we focused on the role of pulsed electric field in large RNA fragments analysis by comparing RNA separation performance in PFCE with that in constant field CE. Separation performance in terms of migration mobility, plate numbers, resolution, and selectivity has been tested for the analysis of RNA from 0.1 to 10.0 kilo nucleotide (knt) under different electrophoretic conditions. Denaturation, important to obtain uniform and identifiable peaks, was accomplished by heating the sample in 4.0M urea prior to analysis and the presence of 4.0M urea in the electrophoresis buffer. Results demonstrate that unlike DNA in PFCE, the pulsed electric field mainly affects the separation performance of RNA between 0.4 and 2.0 knt. The migration mobility of long RNA fragments is not a strong function of modulation depth and pulsed frequency. Moreover, the logarithm of RNA mobility is almost inversely proportional to the logarithm of molecule size up to 6.0 knt with correlation coefficient higher than 0.99 in all the polymer concentrations measured here. Resonance frequency of RNA in PFCE was also observed. While these initial experiments show no distinct advantages of using PFCE for RNA separation, they do take further step toward characterizing the migration behavior of RNA under pulsed field conditions. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Biodegradable Polymers


    Vroman, Isabelle; Tighzert, Lan


    Biodegradable materials are used in packaging, agriculture, medicine and other areas. In recent years there has been an increase in interest in biodegradable polymers. Two classes of biodegradable polymers can be distinguished: synthetic or natural polymers. There are polymers produced from feedstocks derived either from petroleum resources (non renewable resources) or from biological resources (renewable resources). In general natural polymers offer fewer advantages than synthetic polymers. ...

  8. Comparative effect of microwaves and boiling on the denaturation of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Stroop, W.G.; Schaefer, D.C. (Veterans Administration Medical Center, Salt Lake City, UT (USA))


    The effect of heat and microwave denaturation of small volumes of double-stranded plasmid DNA has been compared. Samples of intact plasmid DNA had plasmid DNA linearized by digestion with EcoRI were conventionally denatured in a boiling water bath or denatured by 2450 MHz of microwave energy for 0-300 s. Heat denaturation for periods longer than 120 s caused breakdown of linearized plasmid DNA; however, microwave denaturation for 10-300 s caused no apparent degradation of linearized DNA. Breakdown of DNA forms II and III was noted in plasmid DNA subjected to 300 s of either heat or microwave denaturation but breakdown of forms II and III occurred more quickly with heat than with microwave treatment. Microwave treatment was also found to be better than heat to denature 32P-labeled DNA probes subsequently used to detect homologous DNA samples immobilized on nitrocellulose filters. A microwave-treated 32P-labeled DNA probe was able to hybridize to DNA samples 20 times more dilute than a heat-treated 32P-labeled DNA probe. Depending on the form of DNA to be analyzed, these results indicate that small volumes of DNA solutions and radiolabeled DNA probes can be effectively denatured in a conventional microwave oven.

  9. The generation of denatured reactor plutonium by different options of the fuel cycle

    Energy Technology Data Exchange (ETDEWEB)

    Broeders, C.H.M.; Kessler, G. [Inst. for Neutron Physics and Reactor Technology, Research Center Karlsruhe (Germany)


    Denatured (proliferation resistant) reactor plutonium can be generated in a number of different fuel cycle options. First denatured reactor plutonium can be obtained if, instead of low enriched U-235 PWR fuel, re-enriched U-235/U-236 from reprocessed uranium is used (fuel type A). Also the envisaged existing 2,500 t of reactor plutonium (being generated world wide up to the year 2010), mostly stored in intermediate fuel storage facilities at present, could be converted during a transition phase into denatured reactor plutonium by the options fuel type B and D. Denatured reactor plutonium could have the same safeguards standard as present low enriched (<20% U-235) LWR fuel. It could be incinerated by recycling once or twice in PWRs and subsequently by multi-recycling in FRs (CAPRA type or IFRs). Once denatured, such reactor plutonium could remain denatured during multiple recycling. In a PWR, e.g., denatured reactor plutonium could be destroyed at a rate of about 250 kg/GWey. While denatured reactor plutonium could be recycled and incinerated under relieved IAEA safeguards, neptunium would still have to be monitored by the IAEA in future for all cases in which considerable amounts of neptunium are produced. (orig.)

  10. Highly anomalous energetics of protein cold denaturation linked to folding-unfolding kinetics.

    Directory of Open Access Journals (Sweden)

    M Luisa Romero-Romero

    Full Text Available Despite several careful experimental analyses, it is not yet clear whether protein cold-denaturation is just a "mirror image" of heat denaturation or whether it shows unique structural and energetic features. Here we report that, for a well-characterized small protein, heat denaturation and cold denaturation show dramatically different experimental energetic patterns. Specifically, while heat denaturation is endothermic, the cold transition (studied in the folding direction occurs with negligible heat effect, in a manner seemingly akin to a gradual, second-order-like transition. We show that this highly anomalous energetics is actually an apparent effect associated to a large folding/unfolding free energy barrier and that it ultimately reflects kinetic stability, a naturally-selected trait in many protein systems. Kinetics thus emerges as an important factor linked to differential features of cold denaturation. We speculate that kinetic stabilization against cold denaturation may play a role in cold adaptation of psychrophilic organisms. Furthermore, we suggest that folding-unfolding kinetics should be taken into account when analyzing in vitro cold-denaturation experiments, in particular those carried out in the absence of destabilizing conditions.

  11. Surprisingly high stability of barley lipid transfer protein, LTP1, towards denaturant, heat and proteases

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Winther, J R


    have been suggested as transporters of monomers for cutin synthesis. We have analysed the stability of LTP1 towards denaturant, heat and proteases and found it to be a highly stable protein, which apparently does not denature at temperatures up to 100 degrees C. This high stability may be important...

  12. Interim assessment of the denatured 233U fuel cycle: feasibility and nonproliferation characteristics

    International Nuclear Information System (INIS)

    Abbott, L.S.; Bartine, D.E.; Burns, T.J.


    A fuel cycle that employs 233 U denatured with 238 U and mixed with thorium fertile material is examined with respect to its proliferation-resistance characteristics and its technical and economic feasibility. The rationale for considering the denatured 233 U fuel cycle is presented, and the impact of the denatured fuel on the performance of Light-Water Reactors, Spectral-Shift-Controlled Reactors, Gas-Cooled Reactors, Heavy-Water Reactors, and Fast Breeder Reactors is discussed. The scope of the R, D and D programs to commercialize these reactors and their associated fuel cycles is also summarized and the resource requirements and economics of denatured 233 U cycles are compared to those of the conventional Pu/U cycle. In addition, several nuclear power systems that employ denatured 233 U fuel and are based on the energy center concept are evaluated

  13. Interim assessment of the denatured /sup 233/U fuel cycle: feasibility and nonproliferation characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Abbott, L.S.; Bartine, D.E.; Burns, T.J. (eds.)


    A fuel cycle that employs /sup 233/U denatured with /sup 238/U and mixed with thorium fertile material is examined with respect to its proliferation-resistance characteristics and its technical and economic feasibility. The rationale for considering the denatured /sup 233/U fuel cycle is presented, and the impact of the denatured fuel on the performance of Light-Water Reactors, Spectral-Shift-Controlled Reactors, Gas-Cooled Reactors, Heavy-Water Reactors, and Fast Breeder Reactors is discussed. The scope of the R, D and D programs to commercialize these reactors and their associated fuel cycles is also summarized and the resource requirements and economics of denatured /sup 233/U cycles are compared to those of the conventional Pu/U cycle. In addition, several nuclear power systems that employ denatured /sup 233/U fuel and are based on the energy center concept are evaluated.

  14. Cation-Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride. (United States)

    Ramakrishnan, Saminathan; Krainer, Georg; Grundmeier, Guido; Schlierf, Michael; Keller, Adrian


    The stability of DNA origami nanostructures under various environmental conditions constitutes an important issue in numerous applications, including drug delivery, molecular sensing, and single-molecule biophysics. Here, the effect of Na + and Mg 2+ concentrations on DNA origami stability is investigated in the presence of urea and guanidinium chloride (GdmCl), two strong denaturants commonly employed in protein folding studies. While increasing concentrations of both cations stabilize the DNA origami nanostructures against urea denaturation, they are found to promote DNA origami denaturation by GdmCl. These inverse behaviors are rationalized by a salting-out of Gdm + to the hydrophobic DNA base stack. The effect of cation-induced DNA origami denaturation by GdmCl deserves consideration in the design of single-molecule studies and may potentially be exploited in future applications such as selective denaturation for purification purposes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Use of anionic denaturing detergents to purify insoluble proteins after overexpression

    Directory of Open Access Journals (Sweden)

    Schlager Benjamin


    Full Text Available Background Many proteins form insoluble protein aggregates, called “inclusion bodies”, when overexpressed in E. coli. This is the biggest obstacle in biotechnology. Ever since the reversible denaturation of proteins by chaotropic agents such as urea or guanidinium hydrochloride had been shown, these compounds were predominantly used to dissolve inclusion bodies. Other denaturants exist but have received much less attention in protein purification. While the anionic, denaturing detergent sodiumdodecylsulphate (SDS is used extensively in analytical SDS-PAGE, it has rarely been used in preparative purification. Results Here we present a simple and versatile method to purify insoluble, hexahistidine-tagged proteins under denaturing conditions. It is based on dissolution of overexpressing bacterial cells in a buffer containing sodiumdodecylsulfate (SDS and whole-lysate denaturation of proteins. The excess of detergent is removed by cooling and centrifugation prior to affinity purification. Host- and overexpressed proteins do not co-precipitate with SDS and the residual concentration of detergent is compatible with affinity purification on Ni/NTA resin. We show that SDS can be replaced with another ionic detergent, Sarkosyl, during purification. Key advantages over denaturing purification in urea or guanidinium are speed, ease of use, low cost of denaturant and the compatibility of buffers with automated FPLC. Conclusion Ionic, denaturing detergents are useful in breaking the solubility barrier, a major obstacle in biotechnology. The method we present yields detergent-denatured protein. Methods to refold proteins from a detergent denatured state are known and therefore we propose that the procedure presented herein will be of general application in biotechnology.

  16. Polymer electronics

    CERN Document Server

    Hsin-Fei, Meng


    Polymer semiconductor is the only semiconductor that can be processed in solution. Electronics made by these flexible materials have many advantages such as large-area solution process, low cost, and high performance. Researchers and companies are increasingly dedicating time and money in polymer electronics. This book focuses on the fundamental materials and device physics of polymer electronics. It describes polymer light-emitting diodes, polymer field-effect transistors, organic vertical transistors, polymer solar cells, and many applications based on polymer electronics. The book also disc

  17. Characteristics of denatured rapeseed oil during storage and refining processes

    Directory of Open Access Journals (Sweden)

    Philen, R. M.


    Full Text Available In 1981, toxic oil syndrome, a progressive multi-system disease caused by consumption of rapeseed oil denatured with aniline occurred in Spain. To date, the causal toxic agent or agents remain unknown. Measures of acidity, moisture, impurities, phosphorous, soaps, and spectrophotometric determinations of color at 409 nm were performed. Since fatty acid anilide concentrations in these oils are associated with risk of disease, w e studied the formation of aniline-derived compounds over time after oil denaturation and by oil deodorization temperatures (200ºC, 215ºC, 230ºC, 245ºC, 260ºC, y 270ºC and times (3, 4, 4.5, 5, 5.5 and 6 hours. Formation of fatty acid anilide compounds increased with storage time. Deodorization led to a reduction of total anilides in all the samples, particularly at temperatures above 245ºC. Esters of 3-(N-phenylamino-1,2-propanediol were not detected.En 1981 tuvo lugar en España el llamado «Síndrome del Aceite Tóxico», una enfermedad progresiva multi-sistemática causada por el consumo de aceite de colza desnaturalizado con anilina. Hasta la fecha, el agente o agentes tóxicos causantes permanecen desconocidos. Se han realizado medidas de acidez, humedad, impurezas, fósforo, jabones y determinaciones espectrofotométricas de color a 409 nm. Puesto que las concentraciones de anilidas de los ácidos grasos en estos aceites se asocian al riesgo de padecer la enfermedad, se estudiaron la formación de compuestos derivados de anilina durante el tiempo de desnaturalización y con las temperaturas y tiempos de desodorización (temperaturas: 200ºC, 215ºC, 230ºC, 245ºC, 260ºC, y 270ºC y tiempos: 3, 4, 4.5, 5, 5.5 y 6 horas. La formación de anilidas de ácidos grasos aumenta con el tiempo de almacenamiento. La desodorización conlleva una reducción de la cantidad total de anilidas en todas las muestras, particularmente cuando la temperatura es superior a 245ºC. No fueron

  18. Small angle neutron scattering studies on protein denaturation ...

    Indian Academy of Sciences (India)

    [3] X H Guo, N M Zhao, S H Chen and J Teixeira, Biopolymers 29, 335 (1990). [4] J Kohlbrecher and W Wagner, J. Appl. Crystallogr. 33, 804 (2000). [5] J B Hayter and J Penfold, Coll. Polym. Sci. 261, 1022 (1983). [6] S Chodankar, V K Aswal, J Kohlbrecher, R Vavrin and A G Wagh, J. Phys.: Condens. Matter 19, 326102 ...

  19. Renaturation of the androgen receptor after denaturation in SDS

    International Nuclear Information System (INIS)

    Johnson, M.P.; Young, C.Y.F.; Rowley, D.R.; Tindall, D.J.


    Renaturation of the steroid binding activity of receptor proteins is a potentially useful tool for their purification and analysis. Cytosol was prepared from rat Dunning prostate tumor in buffer containing molybdate and then denatured by addition of SDS buffer and heating. Aliquots were precipitated in cold acetone and the resulting pellets were washed and solubilized with a small volume of solution containing a chaotropic agent such as 6M guanidine, 8M urea, or 5M sodium iodide. After a 20-minute incubation, samples were diluted 20-fold with buffer containing 4nM [ 3 H]dihydrotestosterone with or without excess unlabeled dihydrotestosterone. Diluted samples were incubated at 0 0 C for varying periods of time prior to assay of bound radioactivity using hydroxylapatite. A time-course of renaturation after exposure to guanidine showed a steady increase of specific binding activity during the first 7 hrs post-dilution that remained stable up to 22 hrs. Experiments with guanidine consistently demonstrated that 25-50% of binding activity was recoverable. Preliminary results using urea or sodium iodide were similar. Efforts to optimize recovery and to characterize the renatured androgen receptor are in progress

  20. Thermally responsive silicon nanowire arrays for native/denatured-protein separation

    International Nuclear Information System (INIS)

    Wang Hongwei; Wang Yanwei; Yuan Lin; Wang Lei; Yang Weikang; Wu Zhaoqiang; Li Dan; Chen Hong


    We present our findings of the selective adsorption of native and denatured proteins onto thermally responsive, native-protein resistant poly(N-isopropylacrylamide) (PNIPAAm) decorated silicon nanowire arrays (SiNWAs). The PNIPAAm–SiNWAs surface, which shows very low levels of native-protein adsorption, favors the adsorption of denatured proteins. The amount of denatured-protein adsorption is higher at temperatures above the lower critical solution temperature (LCST) of PNIPAAm. Temperature cycling surrounding the LCST, which ensures against thermal denaturation of native proteins, further increases the amount of denatured-protein adsorption. Moreover, the PNIPAAm–SiNWAs surface is able to selectively adsorb denatured protein even from mixtures of different protein species; meanwhile, the amount of native proteins in solution is kept nearly at its original level. It is believed that these results will not only enrich current understanding of protein interactions with PNIPAAm-modified SiNWAs surfaces, but may also stimulate applications of PNIPAAm–SiNWAs surfaces for native/denatured protein separation. (paper)

  1. Protein denaturation and functional properties of Lenient Steam Injection heat treated whey protein concentrate

    DEFF Research Database (Denmark)

    Dickow, Jonatan Ahrens; Kaufmann, Niels; Wiking, Lars


    Whey protein concentrate (WPC) was heat treated by use of the novel heat treatment method of Lenient Steam Injection (LSI) to elucidate new functional properties in relation to heat-induced gelation of heat treated WPC. Denaturation was measured by both DSC and FPLC, and the results of the two...... methods were highly correlated. Temperatures of up to 90 °C were applicable using LSI, whereas only 68 °C could be reached by plate heat exchange before coagulation/fouling. Denaturation of whey proteins increased with increasing heat treatment temperature up to a degree of 30–35% denaturation at 90 °C...


    NARCIS (Netherlands)

    Morichere, D; Malliaras, G.G; Krasnikov, V.V.; Bolink, H.J; Hadziioannou, G

    The use of polymers as photorefractive materials offers many advantages : flexibility in synthesis, doping, processing and low cost. The required functionalities responsible for photorefractivity, namely charge generation, transport, trapping and linear electrooptic effect are given in the polymer

  3. Kinetics of Thermal Denaturation and Aggregation of Bovine Serum Albumin.

    Directory of Open Access Journals (Sweden)

    Vera A Borzova

    Full Text Available Thermal aggregation of bovine serum albumin (BSA has been studied using dynamic light scattering, asymmetric flow field-flow fractionation and analytical ultracentrifugation. The studies were carried out at fixed temperatures (60°C, 65°C, 70°C and 80°C in 0.1 M phosphate buffer, pH 7.0, at BSA concentration of 1 mg/ml. Thermal denaturation of the protein was studied by differential scanning calorimetry. Analysis of the experimental data shows that at 65°C the stage of protein unfolding and individual stages of protein aggregation are markedly separated in time. This circumstance allowed us to propose the following mechanism of thermal aggregation of BSA. Protein unfolding results in the formation of two forms of the non-native protein with different propensity to aggregation. One of the forms (highly reactive unfolded form, Uhr is characterized by a high rate of aggregation. Aggregation of Uhr leads to the formation of primary aggregates with the hydrodynamic radius (Rh,1 of 10.3 nm. The second form (low reactive unfolded form, Ulr participates in the aggregation process by its attachment to the primary aggregates produced by the Uhr form and possesses ability for self-aggregation with formation of stable small-sized aggregates (Ast. At complete exhaustion of Ulr, secondary aggregates with the hydrodynamic radius (Rh,2 of 12.8 nm are formed. At 60°C the rates of unfolding and aggregation are commensurate, at 70°C the rates of formation of the primary and secondary aggregates are commensurate, at 80°C the registration of the initial stages of aggregation is complicated by formation of large-sized aggregates.

  4. On the Use of Potential Denaturing Agents for Ethanol in Direct Ethanol Fuel Cells

    Directory of Open Access Journals (Sweden)

    Domnik Bayer


    Full Text Available Acidic or alkaline direct ethanol fuel cells (DEFCs can be a sustainable alternative for power generation if they are fuelled with bio-ethanol. However, in order to keep the fuel cheap, ethanol has to be exempted from tax on spirits by denaturing. In this investigation the potential denaturing agents fusel oil, tert-butyl ethyl ether, and Bitrex were tested with regard to their compatibility with fuel cells. Experiments were carried out both in sulphuric acid and potassium hydroxide solution. Beside, basic electrochemical tests, differential electrochemical mass spectrometry (DEMS and fuel cell tests were conducted. It was found that fusel oil is not suitable as denaturing agent for DEFC. However, tert-butyl ethyl ether does not seem to hinder the ethanol conversion as much. Finally, a mixture of tert-butyl ethyl ether and Bitrex can be proposed as promising candidate as denaturing agent for use in acidic and alkaline DEFC.

  5. 27 CFR 19.602 - Marks on containers of completely denatured alcohol. (United States)


    ... number where filled, the contents in wine gallons, the apparent proof, the words “Completely Denatured Alcohol”, and the formula number. (Sec. 201, Pub. L. 85-859, 72 Stat. 1360, as amended) (26 U.S.C. 5206)) ...

  6. How chain length and charge affect surfactant denaturation of acyl coenzyme a binding protein (ACBP)

    DEFF Research Database (Denmark)

    Andersen, Kell; Otzen, Daniel


    Using intrinsic tryptophan fluorescence, equilibria and kinetics of unfolding of acyl coenzyme A binding protein (ACBP) have been investigated in sodium alkyl sulfate surfactants of different chain length (8-16 carbon atoms) and with different proportions of the nonionic surfactant dodecyl...... maltoside (DDM). The aim has been to determine how surfactant chain length and micellar charge affect the denaturation mechanism. ACBP denatures in two steps irrespective of surfactant chain length, but with increasing chain length, the potency of the denaturant rises more rapidly than the critical micelle...... constants increases linearly with denaturant concentration below the cmc but declines at higher concentrations. Both shortening chain length and decreasing micellar charge reduce the overall kinetics of unfolding and makes the dependence of unfolding rate constants on surfactant concentration more complex...

  7. Effects of thermal denaturation on binding between bixin and whey protein. (United States)

    Zhang, Yue; Zhong, Qixin


    Heating is commonly used in the manufacture of dairy products, but impacts of thermal denaturation on binding between whey protein and molecules such as pigments are poorly understood. The objective of this work was to study the impacts of thermal denaturation on binding between bixin, a pigment relevant to colored cheeses, and whey proteins using several complementary techniques. Fluorescence spectroscopy data showed that heat treatment caused tryptophan in β-lactoglobulin and α-lactalbumin to be exposed to a more polar environment, but the opposite was observed for bovine serum albumin. The fluorescence quenching study indicated that the quenching of whey protein fluorescence by bixin was static quenching, and the affinity of binding with bixin was enhanced after thermal denaturation, caused by a higher extent of unordered structures, as revealed by results from circular dichroism and Fourier transform infrared spectra. β-Lactoglobulin was responsible for overall impacts of thermal denaturation on binding between bixin and whey protein isolate.

  8. Polymer Nanocomposites

    Indian Academy of Sciences (India)

    polymer nanocompo- sites are used as advanced toner materials for high quality colour copiers and printers and as contrast agents in NMR analysis, memory devices. .... tions on polymer nanocomposite can thus pay rich dividends. Suggested Reading. [1] Metal-Polymer Nanocomposites Nicolais, Luigi(ed.) ; Carotenuto,.

  9. Improved Denaturation of Small RNA Duplexes and Its Application for Northern Blotting. (United States)

    Harris, C Jake; Baulcombe, David C; Molnar, Attila


    Small RNAs (sRNAs) are short (18-30 nucleotide) noncoding RNA molecules, which control gene expression and pathogen response in eukaryotes. They are associated with and guide nucleases to target nucleic acids by nucleotide base pairing. We found that current techniques for small RNA detection are adversely affected by the presence of complementary RNA. Thus we established FDF-PAGE (fully denaturing formaldehyde polyacrylamide gel electrophoresis), which dramatically improves denaturation efficiency and subsequently the detection of sequestered sRNAs.

  10. Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique.


    Noll, W W; Collins, M


    Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. We have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and th...

  11. Effect of mechanical denaturation on surface free energy of protein powders. (United States)

    Mohammad, Mohammad Amin; Grimsey, Ian M; Forbes, Robert T; Blagbrough, Ian S; Conway, Barbara R


    Globular proteins are important both as therapeutic agents and excipients. However, their fragile native conformations can be denatured during pharmaceutical processing, which leads to modification of the surface energy of their powders and hence their performance. Lyophilized powders of hen egg-white lysozyme and β-galactosidase from Aspergillus oryzae were used as models to study the effects of mechanical denaturation on the surface energies of basic and acidic protein powders, respectively. Their mechanical denaturation upon milling was confirmed by the absence of their thermal unfolding transition phases and by the changes in their secondary and tertiary structures. Inverse gas chromatography detected differences between both unprocessed protein powders and the changes induced by their mechanical denaturation. The surfaces of the acidic and basic protein powders were relatively basic, however the surface acidity of β-galactosidase was higher than that of lysozyme. Also, the surface of β-galactosidase powder had a higher dispersive energy compared to lysozyme. The mechanical denaturation decreased the dispersive energy and the basicity of the surfaces of both protein powders. The amino acid composition and molecular conformation of the proteins explained the surface energy data measured by inverse gas chromatography. The biological activity of mechanically denatured protein powders can either be reversible (lysozyme) or irreversible (β-galactosidase) upon hydration. Our surface data can be exploited to understand and predict the performance of protein powders within pharmaceutical dosage forms. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Interim assessment of the denatured /sup 233/U fuel cycle: feasibility and nonproliferation characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Abbott, L.S.; Bartine, D.E.; Burns, T.J. (eds.)


    A fuel cycle that employs /sup 233/U denatured with /sup 238/U and mixed with thorium fertile material is examined with respect to its proliferation-resistance characteristics and its technical and economic feasibility. The rationale for considering the denatured /sup 233/U fuel cycle is presented, and the impact of the denatured fuel on the performance of Light-Water Reactors, Spectral-Shift-Controlled Reactors, Gas-Cooled Reactors, Heavy-Water Reactors, and Fast Breeder Reactors is discussed. The scope of the R, D and D programs to commercialize these reactors and their associated fuel cycles is also summarized and the resource requirements and economics of denatured /sup 233/U cycles are compared to those of the conventional Pu/U cycle. In addition, several nuclear power systems that employ denatured /sup 233/U fuel and are based on the energy center concept are evaluated. Under this concept, dispersed power reactors fueled with denatured or low-enriched uranium fuel are supported by secure energy centers in which sensitive activities of the nuclear cycle are performed. These activities include /sup 233/U production by Pu-fueled transmuters (thermal or fast reactors) and reprocessing. A summary chapter presents the most significant conclusions from the study and recommends areas for future work.

  13. Interim assessment of the denatured 233U fuel cycle: feasibility and nonproliferation characteristics

    International Nuclear Information System (INIS)

    Abbott, L.S.; Bartine, D.E.; Burns, T.J.


    A fuel cycle that employs 233 U denatured with 238 U and mixed with thorium fertile material is examined with respect to its proliferation-resistance characteristics and its technical and economic feasibility. The rationale for considering the denatured 233 U fuel cycle is presented, and the impact of the denatured fuel on the performance of Light-Water Reactors, Spectral-Shift-Controlled Reactors, Gas-Cooled Reactors, Heavy-Water Reactors, and Fast Breeder Reactors is discussed. The scope of the R, D and D programs to commercialize these reactors and their associated fuel cycles is also summarized and the resource requirements and economics of denatured 233 U cycles are compared to those of the conventional Pu/U cycle. In addition, several nuclear power systems that employ denatured 233 U fuel and are based on the energy center concept are evaluated. Under this concept, dispersed power reactors fueled with denatured or low-enriched uranium fuel are supported by secure energy centers in which sensitive activities of the nuclear cycle are performed. These activities include 233 U production by Pu-fueled transmuters (thermal or fast reactors) and reprocessing. A summary chapter presents the most significant conclusions from the study and recommends areas for future work

  14. Effects of protein and phosphate buffer concentrations on thermal denaturation of lysozyme analyzed by isoconversional method. (United States)

    Cao, X M; Tian, Y; Wang, Z Y; Liu, Y W; Wang, C X


    Thermal denaturation of lysozymes was studied as a function of protein concentration, phosphate buffer concentration, and scan rate using differential scanning calorimetry (DSC), which was then analyzed by the isoconversional method. The results showed that lysozyme thermal denaturation was only slightly affected by the protein concentration and scan rate. When the protein concentration and scan rate increased, the denaturation temperature (Tm) also increased accordingly. On the contrary, the Tm decreased with the increase of phosphate buffer concentration. The denaturation process of lysozymes was accelatated and the thermal stability was reduced with the increase of phosphate concentration. One part of degeneration process was not reversible where the aggregation occurred. The other part was reversible. The apparent activation energy (Ea) was computed by the isoconversional method. It decreased with the increase of the conversion ratio (α). The observed denaturation process could not be described by a simple reaction mechanism. It was not a process involving 2 standard reversible states, but a multi-step process. The new opportunities for investigating the kinetics process of protein denaturation can be supplied by this novel isoconversional method.

  15. Large-Area Nanoscale Patterning of Functional Materials by Nanomolding in Capillaries

    NARCIS (Netherlands)

    Duan, X.; Zhao, Yiping; Berenschot, Johan W.; Tas, Niels Roelof; Reinhoudt, David; Huskens, Jurriaan


    Within the past years there has been much effort in developing and improving new techniques for the nanoscale patterning of functional materials used in promising applications like nano(opto)electronics. Here a high-resolution soft lithography technique—nanomolding in capillaries (NAMIC)—is

  16. Polymer Chemistry (United States)

    Williams, Martha; Roberson, Luke; Caraccio, Anne


    This viewgraph presentation describes new technologies in polymer and material chemistry that benefits NASA programs and missions. The topics include: 1) What are Polymers?; 2) History of Polymer Chemistry; 3) Composites/Materials Development at KSC; 4) Why Wiring; 5) Next Generation Wiring Materials; 6) Wire System Materials and Integration; 7) Self-Healing Wire Repair; 8) Smart Wiring Summary; 9) Fire and Polymers; 10) Aerogel Technology; 11) Aerogel Composites; 12) Aerogels for Oil Remediation; 13) KSC's Solution; 14) Chemochromic Hydrogen Sensors; 15) STS-130 and 131 Operations; 16) HyperPigment; 17) Antimicrobial Materials; 18) Conductive Inks Formulations for Multiple Applications; and 19) Testing and Processing Equipment.

  17. Star Polymers. (United States)

    Ren, Jing M; McKenzie, Thomas G; Fu, Qiang; Wong, Edgar H H; Xu, Jiangtao; An, Zesheng; Shanmugam, Sivaprakash; Davis, Thomas P; Boyer, Cyrille; Qiao, Greg G


    Recent advances in controlled/living polymerization techniques and highly efficient coupling chemistries have enabled the facile synthesis of complex polymer architectures with controlled dimensions and functionality. As an example, star polymers consist of many linear polymers fused at a central point with a large number of chain end functionalities. Owing to this exclusive structure, star polymers exhibit some remarkable characteristics and properties unattainable by simple linear polymers. Hence, they constitute a unique class of technologically important nanomaterials that have been utilized or are currently under audition for many applications in life sciences and nanotechnologies. This article first provides a comprehensive summary of synthetic strategies towards star polymers, then reviews the latest developments in the synthesis and characterization methods of star macromolecules, and lastly outlines emerging applications and current commercial use of star-shaped polymers. The aim of this work is to promote star polymer research, generate new avenues of scientific investigation, and provide contemporary perspectives on chemical innovation that may expedite the commercialization of new star nanomaterials. We envision in the not-too-distant future star polymers will play an increasingly important role in materials science and nanotechnology in both academic and industrial settings.

  18. Polymer Electrolytes (United States)

    Hallinan, Daniel T.; Balsara, Nitash P.


    This review article covers applications in which polymer electrolytes are used: lithium batteries, fuel cells, and water desalination. The ideas of electrochemical potential, salt activity, and ion transport are presented in the context of these applications. Potential is defined, and we show how a cell potential measurement can be used to ascertain salt activity. The transport parameters needed to fully specify a binary electrolyte (salt + solvent) are presented. We define five fundamentally different types of homogeneous electrolytes: type I (classical liquid electrolytes), type II (gel electrolytes), type III (dry polymer electrolytes), type IV (dry single-ion-conducting polymer electrolytes), and type V (solvated single-ion-conducting polymer electrolytes). Typical values of transport parameters are provided for all types of electrolytes. Comparison among the values provides insight into the transport mechanisms occurring in polymer electrolytes. It is desirable to decouple the mechanical properties of polymer electrolyte membranes from the ionic conductivity. One way to accomplish this is through the development of microphase-separated polymers, wherein one of the microphases conducts ions while the other enhances the mechanical rigidity of the heterogeneous polymer electrolyte. We cover all three types of conducting polymer electrolyte phases (types III, IV, and V). We present a simple framework that relates the transport parameters of heterogeneous electrolytes to homogeneous analogs. We conclude by discussing electrochemical stability of electrolytes and the effects of water contamination because of their relevance to applications such as lithium ion batteries.

  19. Transurethral radiofrequency collagen denaturation for the treatment of women with urinary incontinence. (United States)

    Kang, Diana; Han, Julia; Neuberger, Molly M; Moy, M Louis; Wallace, Sheila A; Alonso-Coello, Pablo; Dahm, Philipp


    Transurethral radiofrequency collagen denaturation is a relatively novel, minimally invasive device-based intervention used to treat individuals with urinary incontinence (UI). No systematic review of the evidence supporting its use has been published to date. To evaluate the efficacy of transurethral radiofrequency collagen denaturation, compared with other interventions, in the treatment of women with UI.Review authors sought to compare the following.• Transurethral radiofrequency collagen denaturation versus no treatment/sham treatment.• Transurethral radiofrequency collagen denaturation versus conservative physical treatment.• Transurethral radiofrequency collagen denaturation versus mechanical devices (pessaries for UI).• Transurethral radiofrequency collagen denaturation versus drug treatment.• Transurethral radiofrequency collagen denaturation versus injectable treatment for UI.• Transurethral radiofrequency collagen denaturation versus other surgery for UI. We conducted a systematic search of the Cochrane Incontinence Group Specialised Register (searched 19 December 2014), EMBASE and EMBASE Classic (January 1947 to 2014 Week 50), Google Scholar and three trials registries in December 2014, along with reference checking. We sought to identify unpublished studies by handsearching abstracts of major gynaecology and urology meetings, and by contacting experts in the field and the device manufacturer. Randomised and quasi-randomised trials of transurethral radiofrequency collagen denaturation versus no treatment/sham treatment, conservative physical treatment, mechanical devices, drug treatment, injectable treatment for UI or other surgery for UI in women were eligible. We screened search results and selected eligible studies for inclusion. We assessed risk of bias and analysed dichotomous variables as risk ratios (RRs) with 95% confidence intervals (CIs) and continuous variables as mean differences (MDs) with 95% CIs. We rated the quality of

  20. Polymer chemistry (revised edition)

    International Nuclear Information System (INIS)

    Kim, Jae Mum


    This book deals with polymer chemistry, which is divided into fourteen chapters. The contents of this book are development of polymer chemistry, conception of polymer, measurement of polymer chemistry, conception of polymer, measurement of polymer, molecule structure of polymer, thermal prosperities of solid polymer, basic theory of polymerization, radical polymerization, ion polymerization, radical polymerization, copolymerization, polymerization by step-reaction, polymer reaction, crown polymer and inorganic polymer on classification and process of creation such as polymeric sulfur and carbon fiber.

  1. Drying and denaturation characteristics of whey protein isolate in the presence of lactose and trehalose. (United States)

    Haque, M Amdadul; Chen, Jie; Aldred, Peter; Adhikari, Benu


    The denaturation kinetics of whey protein isolate (WPI), in the presence and absence of lactose and trehalose, was quantified in a convective air-drying environment. Single droplets of WPI, WPI-lactose and WPI-trehalose were dried in conditioned air (2.5% RH, 0.5m/s air velocity) at two temperatures (65°C and 80°C) for 500s. The initial solid concentration of these solutions was 10% (w/v) in all the samples. Approximately 68% of WPI was denatured when it was dried in the absence of sugars. Addition of 20% trehalose prevented the irreversible denaturation of WPI at both temperatures. Thirty percent lactose was required to prevent denaturation of WPI at 65°C and the same amount of lactose protected only 70% of WPI from denaturation at 80°C. The secondary structures of WPI were found to be altered by the drying-induced stresses, even in the presence of 20% trehalose and 30% lactose. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Alcohol-induced structural transitions in the acid-denatured Bacillus licheniformis α-amylase

    Directory of Open Access Journals (Sweden)

    Adyani Azizah Abd Halim


    Full Text Available Alcohol-induced structural changes in the acid-denatured Bacillus licheniformis α-amylase (BLA at pH 2.0 were studied by far-ultra violet circular dichroism, intrinsic, three-dimensional and 8-anilino-1-naphthalene sulfonic acid (ANS fluorescence, acrylamide quenching and thermal denaturation. All the alcohols used in this study produced partial refolding in the acid-denatured BLA as evident from the increased mean residue ellipticity at 222 nm, increased intrinsic fluorescence and decreased ANS fluorescence. The order of effectiveness of these alcohols to induce a partially folded state of BLA was found to be: 2,2,2-trifluoroethanol/tert-butanol > 1-propanol/2-propanol > 2-chloroethanol > ethanol > methanol. Three-dimensional fluorescence and acrylamide quenching results obtained in the presence of 5.5 M tert-butanol also suggested formation of a partially folded state in the acid-denatured BLA. However, 5.5 M tert-butanol-induced state of BLA showed a non-cooperative thermal transition. All these results suggested formation of a partially folded state of the acid-denatured BLA in the presence of these alcohols. Furthermore, their effectiveness was found to be guided by their chain length, position of methyl groups and presence of the substituents.

  3. Advanced portrayal of SMIL coating by allying CZE performance with in-capillary topographic and charge-related surface characterization

    Energy Technology Data Exchange (ETDEWEB)

    Stock, Lorenz G. [Division of Chemistry and Bioanalytics, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Leitner, Michael; Traxler, Lukas [Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz (Austria); Bonazza, Klaus [Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Vienna (Austria); Leclercq, Laurent; Cottet, Hervé [Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, Place Eugène Bataillon, CC 1706, 34095 Montpellier (France); Friedbacher, Gernot [Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Vienna (Austria); Ebner, Andreas [Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz (Austria); Stutz, Hanno, E-mail: [Division of Chemistry and Bioanalytics, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, Hellbrunnerstrasse 34, 5020 Salzburg (Austria)


    A successive multiple ionic polymer layer (SMIL) coating composed of four layers improved the capillary electrophoretic separation of a recombinant major birch pollen allergen and closely related variants when poly(acrylamide-co-2-acrylamido-2-methyl-1-propansulfonate) (55% PAMAMPS) replaced dextran sulfate as terminal SMIL layer. 55% PAMAMPS decelerated the electroosmotic flow (EOF) due to its lower charge density. Atomic force microscopy (AFM) was used to investigate SMIL properties directly on the inner capillary surface and to relate them to EOF measurements and results of associated CZE separations of a mixture of model proteins and peptides that were performed in the same capillary. For the first time, AFM-based biosensing topography and recognition imaging mode (TREC) under liquid conditions was applied for a sequential characterization of the inner surface of a SMIL coated capillary after selected treatments including pristine SMIL, SMIL after contact with the model mixture, after alkaline rinsing, and the replenishment of the terminal polyelectrolyte layer. A cantilever with tip-tethered avidin was used to determine the charge homogeneity of the SMIL surface in the TREC mode. SMIL coated rectangular capillaries with 100 μm internal diameter assured accessibility of the inner surface for this cantilever type. Observed changes in CZE performance and EOF mobility during capillary treatment were also reflected by alterations in surface roughness and charge distribution of the SMIL coating. A renewal of the terminal SMIL layer restored the original surface properties of SMIL and the separation performance. The alliance of the novel TREC approach and CZE results allows for an improved understanding and a comprehensive insight in effects occurring on capillary coatings. - Highlights: • SMIL coating with a terminal layer of reduced charge density improves CZE separation. • Capillaries with rectangular diameter allow for in-capillary TREC-AFM measurement.

  4. Polymer Nanocomposites

    Indian Academy of Sciences (India)

    thane, PVC, polyesters, polystyrene and polypropylene. Also, some biocompatible polymers like PLA, poly (E-caprolactone) to mention a few, have been synthesized by varying methods and with different clay loadings (%by weight). The hydrophobicity /hydrophilicity ofthe polymer affects its dispersion in the clay.


    Directory of Open Access Journals (Sweden)

    Heriberto Molina-Pérez


    Full Text Available This work presents an approach to match the foaling thickness of dairy food and the concentration of denatured β-lg (β-lactoglobuline by a mathematical model. This includes, on the one hand, the dynamic simulation of fouling and, on the other hand, the generation of denatured β-lg under a kinetic model. In both cases a transient energy balance is developed, including the rigorous calculation of the global coefficient, and the properties by the Choi-Okos model. The solution was obtained by a fourth order Runge-Kutta written in Excel’s Macro language Visual Basic. The equivalence concluded with a model obtained by a non-linear multiple regression that relates the concentration of denatured β-lg and the foaling thickness. This methodology is applicable to analysis equipment cleaning in which kinetic cleaning has equality by reduction of the foaling thickness.

  6. Dual-mode computer processing for high resolution DNA thermal denaturation experiments. (United States)

    Ansevin, A T; Vizard, D L


    Two modes of data processing are appropriate in conducting high resolution thermal denaturation experiments (thermal increments of 0.05 degrees or closer). In the first mode, a general purpose microcomputer provides on-line services important to the control and monitoring of the initial experiment, including control of the spectrophotometer and heater, the recording of data, and the display of current hyperchromicities and approximate first derivatives. A subsequent microcomputer program then reads the recorded data files and carries out accurate calculations of derivative denaturation profiles and the estimate of the statistical error of the first derivative at each point. The data collection program handles three samples at a time and was designed to provide optimal results in thermal denaturation experiments with a single-beam spectrophotometer.

  7. Intrinsic alterations in the partial molar volume on the protein denaturation: surficial Kirkwood-Buff approach. (United States)

    Yu, Isseki; Takayanagi, Masayoshi; Nagaoka, Masataka


    The partial molar volume (PMV) of the protein chymotrypsin inhibitor 2 (CI2) was calculated by all-atom MD simulation. Denatured CI2 showed almost the same average PMV value as that of native CI2. This is consistent with the phenomenological question of the protein volume paradox. Furthermore, using the surficial Kirkwood-Buff approach, spatial distributions of PMV were analyzed as a function of the distance from the CI2 surface. The profiles of the new R-dependent PMV indicate that, in denatured CI2, the reduction in the solvent electrostatic interaction volume is canceled out mainly by an increment in thermal volume in the vicinity of its surface. In addition, the PMV of the denatured CI2 was found to increase in the region in which the number density of water atoms is minimum. These results provide a direct and detailed picture of the mechanism of the protein volume paradox suggested by Chalikian et al.

  8. Inhibition of thermal induced protein denaturation of extract/fractions of Withania somnifera and isolated withanolides. (United States)

    Khan, Murad Ali; Khan, Haroon; Rauf, Abdul; Ben Hadda, Taibi


    This study describes the in vitro inhibition of protein denaturation of extract/fractions of Withania somnifera and isolated withanolides including 20β hydroxy-1-oxo(22R)-witha-2,5,24 trienolide (1), (20R,22R-14α,20α)-dihydroxy-1-oxowitha-2,5,16,24 tetraenolide (2). The results showed that the extract/fractions of the plant evoked profound inhibitory effect on thermal-induced protein denaturation. The chloroform fraction caused the most dominant attenuation of 68% at 500 μg/mL. The bioactivity-guided isolation from chloroform fraction led to the isolation of compounds 1 and 2 that showed profound protein inhibition with 78.05% and 80.43% effect at 500 μg/mL and thus strongly complimented the activity of extract/fractions. In conclusion, extract/fractions of W. somnifera possessed strong inhibition of protein denaturation that can be attributed to these isolated withanolides.

  9. Nonsurgical Transurethral Radiofrequency Collagen Denaturation: Results at Three Years after Treatment

    Directory of Open Access Journals (Sweden)

    Denise M. Elser


    Full Text Available Objective. To assess treatment efficacy and quality of life in women with stress urinary incontinence 3 years after treatment with nonsurgical transurethral radiofrequency collagen denaturation. Methods. This prospective study included 139 women with stress urinary incontinence due to bladder outlet hypermobility. Radiofrequency collagen denaturation was performed using local anesthesia in an office setting. Assessments included incontinence quality of life (I-QOL and urogenital distress inventory (UDI-6 instruments. Results. In total, 139 women were enrolled and 136 women were treated (mean age, 47 years. At 36 months, intent-to-treat analysis (n=139 revealed significant improvements in quality of life. Mean I-QOL score improved 17 points from baseline (P=.0004, while mean UDI-6 score improved (decreased 19 points (P=.0005. Conclusions. Transurethral collagen denaturation is a low-risk, office-based procedure that results in durable quality-of-life improvements in a significant proportion of women for as long as 3 years.

  10. Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique

    International Nuclear Information System (INIS)

    Noll, W.W.; Collins, M.


    Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. The authors have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and the reaction mixture is electrophoresed on a denaturing gradient gel. Only the genomic DNA probe hybrids migrate into the gel. Differences in hybrid mobility on the gel indicate base pair changes in the genomic DNA. They have used this technique to identify two polymorphic sites within a 1.2-kilobase region of human chromosome 20. This approach should greatly facilitate the identification of DNA polymorphisms useful for gene linkage studies and the diagnosis of genetic diseases

  11. Chemical denaturation of globular proteins at the air-water interface

    International Nuclear Information System (INIS)

    Perriman, A.; White, J.; Henderson, M.


    X-ray and neutron reflectometry has been used to probe the equilibrium surface structure of hen egg white lysozyme (lysozyme) and bovine β -lactoglobulin (β -lactoglobulin) under denaturing conditions at the air-water interface. This was achieved by performing experiments on 10 mg mL -1 protein solutions containing increasing concentrations of guanidinium hydrochloride For solutions containing no G.HCl, the surface structure of the proteins was represented by a two-layer model with total thicknesses of 48 Angstroms and 38 Angstroms for lysozyme and β -lactoglobulin, respectively. The total volume of a single protein molecule and the associated water molecules was determined to be approximately 45 (0.3) nm 3 for lysozyme, and 60 (0.3) nm 3 for β -lactoglobulin. The thickness dimensions and the total volumes compared favourably with the crystal dimensions of 45 x 30 x 30 Angstroms (40.5 nm 3 ), and 36 x 36 x 36 Angstroms (47 nm 3 ) for lysozyme and β -lactoglobulin, respectively. This comparison suggests that when no denaturant was present, the structures of lysozyme and β -lactoglobulin were near to their native conformations at the air-water The response to the presence of the chemical denaturant was different for each protein. The surface layer of β -lactoglobulin expanded at very low concentrations (0.2 mol dm -3 ) of G.HCl, where the lysozyme layer contracted. At higher concentrations, unfolding of both the proteins led to the formation of a third diffuse layer. In general, lysozyme appeared to be less responsive to the chemical denaturant, which is most likely a result of the higher disulfide content of lysozyme. A protocol allowing quantitative analysis of the contribution from the air-water interface to the chemical denaturation of a protein was developed. The protocol involved calculation of the Gibbs free energy of a protein at zero denaturant concentration, by using the change in the adsorbed layer thickness as an order parameter

  12. Isoenergic modification of whey protein structure by denaturation and crosslinking using transglutaminase

    DEFF Research Database (Denmark)

    Stender, Emil G. P.; Koutina, Glykeria; Almdal, Kristoffer


    Transglutaminase (TG) catalyzes formation of covalent bonds between lysine and glutamine side chains and has applications in manipulation of food structure. Physical properties of a whey protein mixture (SPC) denatured either at elevated pH or by heat-treatment and followed by TG catalyzed......, thus heating caused the largest exposure of the hydrophobic core of SPC proteins, which was decreased by crosslinking. The particle size of the treated SPC samples increased upon crosslinking by TG. Moreover, the particle morphology depended on the type of denaturing treatment, thus heat-treated SPC...

  13. Reversible Dimerization of Acid-Denatured ACBP Controlled by Helix A4

    DEFF Research Database (Denmark)

    Fieber, Wolfgang; Kragelund, Birthe Brandt; Meldal, Morten Peter


    denaturing conditions at pH 2.3, helix conformations are still populated in 24% of the ensemble of molecules. The structure of HA4 at atomic resolution was assessed using nuclear magnetic resonance (NMR) spectroscopy. Long-range NOEs between remote residues at opposite peptide ends suggested the formation...... of dimers and revealed a cooperative stabilization of helix A4 in this process. This emphasizes its special role in the structure formation in the denatured state of ACBP. No dimers are formed in the presence of guanidine hydrochloride, which underlines the fundamental difference between the nature...

  14. Atomic level description of the protecting effect of osmolytes against thermal denaturation of proteins (United States)

    Pieraccini, Stefano; Burgi, Luigi; Genoni, Alessandro; Benedusi, Anna; Sironi, Maurizio


    The protecting effect of the osmolyte molecule taurine against thermal denaturation of the protein Chimotripsin Inhibitor 2 was modelled using Molecular Dynamics simulations. The protein was simulated in denaturing conditions at different taurine concentrations. Analysis of the molecular details of its behaviour shows that the protective effect of the osmolyte is concentration dependent. Moreover, the influence of taurine on the solvent structure was studied. A concentration dependent ordering effect of taurine on water molecules emerges from solvent structure analysis and is well correlated to the protecting effect observed. Based on these observations an interpretation of the osmoprotective effect is proposed.

  15. Sensitive spectroscopic detection of large and denatured protein aggregates in solution by use of the fluorescent dye Nile re

    NARCIS (Netherlands)

    Sutter, M.; Oliveira, S.; Sanders, N.N.; Lucas, B.; Hoek, van A.; Hink, M.A.; Visser, A.J.W.G.; Smedt, de S.C.; Hennink, W.E.; Jiskoot, W.


    The fluorescent dye Nile red was used as a probe for the sensitive detection of large, denatured aggregates of the model protein ß-galactosidase (E. coli) in solution. Aggregates were formed by irreversible heat denaturation of ß-galactosidase below and above the protein¿s unfolding temperature of

  16. Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Kristjansdottir, Sigridur; Teilum, Kaare


    The denatured state of a protein contains important information about the determinants of the folding process. By combining site-directed spin-labeling NMR experiments and restrained computer simulations, we have determined ensembles of conformations that represent the denatured state of the bovi...

  17. Formation of Native and Non-native Interactions in Ensembles of Denatured ACBP Molecules from Paramagnetic Relaxation Enhancement Studies

    DEFF Research Database (Denmark)

    Kristjansdottir, S.; Lindorff-Larsen, Kresten; Fieber, W.


    in the denatured states with those in the transition state for folding we also provided new insights into the mechanism of formation of the native state of this protein. Keywords: protein folding; denatured state; NMR; molecular dynamics; structural studies Abbreviations: ACBP, acyl coenzyme A binding protein; Gu...

  18. Reversible denaturation of Brazil nut 2S albumin (Ber e1) and implication of structural destabilization on digestion by pepsin

    NARCIS (Netherlands)

    Koppelman, S.J.; Nieuwenhuizen, W.F.; Gaspari, M.; Knippels, L.M.J.; Penninks, A.H.; Knol, E.F.; Hefle, S.L.; Jongh,


    The high resistance of Brazil nut 2S albumin, previously identified as an allergen, against proteolysis by pepsin was examined in this work. Although the denaturation temperature of this protein exceeds the 110 °C at neutral pH, at low pH a fully reversible thermal denaturation was observed at ∼82

  19. Urea and Guanidinium Induced Denaturation of a Trp-Cage Miniprotein

    Czech Academy of Sciences Publication Activity Database

    Heyda, Jan; Kožíšek, Milan; Bednárová, Lucie; Thompson, G.; Konvalinka, Jan; Vondrášek, Jiří; Jungwirth, Pavel


    Roč. 115, č. 28 (2011), s. 8910-8924 ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GA203/08/0114 Institutional research plan: CEZ:AV0Z40550506 Keywords : trp-cage denaturation * urea * guanidinium * molecular dynamics Subject RIV: CC - Organic Chemistry Impact factor: 3.696, year: 2011

  20. Protecting role of cosolvents in protein denaturation by SDS: a structural study

    Directory of Open Access Journals (Sweden)

    Wouters Johan


    Full Text Available Abstract Background Recently, we reported a unique approach to preserve the activity of some proteins in the presence of the denaturing agent, Sodium Dodecyl Sulfate (SDS. This was made possible by addition of the amphipathic solvent 2,4-Methyl-2-PentaneDiol (MPD, used as protecting but also as refolding agent for these proteins. Although the persistence of the protein activity in the SDS/MPD mixture was clearly established, preservation of their structure was only speculative until now. Results In this paper, a detailed X-ray study addresses the pending question. Crystals of hen egg-white lysozyme were grown for the first time in the presence of MPD and denaturing concentrations of SDS. Depending on crystallization conditions, tetragonal crystals in complex with either SDS or MPD were collected. The conformation of both structures was very similar to the native lysozyme and the obtained complexes of SDS-lysozyme and MPD-lysozyme give some insights in the interplay of protein-SDS and protein-MPD interactions. Conclusion This study clearly established the preservation of the enzyme structure in a SDS/MPD mixture. It is hypothesized that high concentrations of MPD would change the properties of SDS and lower or avoid interactions between the denaturant and the protein. These structural data therefore support the hypothesis that MPD avoids disruption of the enzyme structure by SDS and can protect proteins from SDS denaturation.

  1. 9 CFR 325.11 - Inedible articles: denaturing and other means of identification; exceptions. (United States)


    ... section, animal food packed in hermetically sealed, retort processed, conventional retail-size containers... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Inedible articles: denaturing and other means of identification; exceptions. 325.11 Section 325.11 Animals and Animal Products FOOD SAFETY...

  2. A Role For Ca 2+ in the Thermal and Urea Denaturation of ...

    African Journals Online (AJOL)

    The stability towards thermal and urea denaturation of haemocyanin from aestivating and nonaestivating A. achatina has been investigated using UV spectroscopy. Thermodynamic parameters calculated show a complex process with two sets of activation energy (Ea); 4.64kcal/mol, 14.39kcal/mol for nonaestivating and ...

  3. Revealing genetic diversity of eukaryotic microorganisms in aquatic environments by denaturing gradient gel electrophoresis

    NARCIS (Netherlands)

    Van Hannen, E.J.; Van Agterveld, M.P.; Gons, H.J.; Laanbroek, H.J.


    A new Eucarya-specific 18S rDNA primer set was constructed and tested using denaturing gradient gel electrophoresis to analyze the genetic diversity of eukaryotic microorganisms in aquatic environments. All eukaryal lines of descent exhibited four or fewer nucleotide mismatches in the forward primer

  4. Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients

    NARCIS (Netherlands)

    Zijnge, V.; Harmsen, H.J.M.; Kleinfelder, J.W.; Rest, M.E. van der; Degener, J.E.; Welling, G.W.

    Bacteria are involved in the onset and progression of periodontitis. A promising molecular technique, denaturing gradient gel electrophoresis (DGGE), to study microbial population dynamics in the subgingival pocket is presented. Twenty-three samples were taken from the subgingival pockets of nine

  5. Denaturing gradient gel electrophoresis as a diagnostic tool in periodontal microbiology

    NARCIS (Netherlands)

    Zijnge, Vincent; Welling, Gjalt W.; Degener, John E.; van Winkelhoff, Arie Jan; Abbas, Frank; Harmsen, Hermie J. M.


    Bacteria play an important role in the initiation and progression of periodontal diseases and are part of a biofilm, which can contain over 100 different species. The aim of the present study was to show the potential of denaturing gradient gel electrophoresis (DGGE) as a tool for the detection of

  6. Resistance to DNA denaturation in irradiated Chinese hamster V79 fibroblasts is linked to cell shape

    International Nuclear Information System (INIS)

    Olive, P.L.; Vanderbyl, S.; MacPhail, S.H.


    Exponentially growing Chinese hamster V79-171b lung fibroblasts seeded at high density on plastic (approximately 7 x 10(3) cells/cm2) flatten, elongate, and produce significant amounts of extracellular fibronectin. When lysed in weak alkali/high salt, the rate of DNA denaturation following exposure to ionizing radiation is exponential. Conversely, cells plated at low density (approximately 7 x 10(2) cells/cm2) on plastic are more rounded 24 h later, produce little extracellular fibronectin, and display unusual DNA denaturation kinetics after X-irradiation. DNA in these cells resists denaturation, as though constraints to DNA unwinding have developed. Cell doubling time and distribution of cells in the growth cycle are identical for both high and low density cultures as is cell survival in response to radiation damage. The connection between DNA conformation and cell shape was examined further in low density cultures grown in conditioned medium. Under these conditions, cells at low density were able to elongate, and DNA denaturation of low density cultures was identical to that of high density cultures. Conversely, cytochalasin D, which interferes with actin polymerization causing cells to round up and release fibronectin, allowed development of constraints in high density cultures. These results suggest that DNA conformation is sensitive to changes in cell shape which result when cells are grown in different environments. However, these changes in DNA conformation detected by the DNA unwinding assay do not appear to play a direct role in radiation-induced cell killing

  7. Identification of denatured enzyme proteins in sodium dodecyl sulfate polyacrylamide gels

    NARCIS (Netherlands)

    Hakvoort, T. B.; Veyron, P.; Muilerman, H. G.; van Dijk, W.; Tager, J. M.


    A simple modification of the immunological sandwich method of Muilerman et al. for the identification of denatured enzyme proteins in sodium dodecyl sulfate-polyacrylamide gels is described, enabling the method to be used in principle for any enzyme whose activity is not inhibited by binding to

  8. Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison

    Energy Technology Data Exchange (ETDEWEB)

    Dahlen, Oda, E-mail:; Erp, Titus S. van, E-mail: [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117 7491 Trondheim (Norway)


    Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimental data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones.

  9. Improvement of fragment and primer selection for mutation detection by denaturing gradient gel electrophoresis

    NARCIS (Netherlands)

    Wu, Y; Hayes, VM; Osinga, J; Mulder, IM; Looman, MWG; Buys, CHCM; Hofstra, RMW


    Denaturing gradient gel electrophoresis (DGGE) is one of the most powerful methods for mutation detection currently available. For successful application the appropriate selection of PCR fragments and PCR primers is crucial. The sequence of interest should always be within the domain with the lowest

  10. Comparative analyses of amplicon migration behavior in differing denaturing gradient gel electrophoresis (DGGE) systems (United States)

    Thornhill, D. J.; Kemp, D. W.; Sampayo, E. M.; Schmidt, G. W.


    Denaturing gradient gel electrophoresis (DGGE) is commonly utilized to identify and quantify microbial diversity, but the conditions required for different electrophoretic systems to yield equivalent results and optimal resolution have not been assessed. Herein, the influence of different DGGE system configuration parameters on microbial diversity estimates was tested using Symbiodinium, a group of marine eukaryotic microbes that are important constituents of coral reef ecosystems. To accomplish this, bacterial clone libraries were constructed and sequenced from cultured isolates of Symbiodinium for the ribosomal DNA internal transcribed spacer 2 (ITS2) region. From these, 15 clones were subjected to PCR with a GC clamped primer set for DGGE analyses. Migration behaviors of the resulting amplicons were analyzed using a range of conditions, including variation in the composition of the denaturing gradient, electrophoresis time, and applied voltage. All tests were conducted in parallel on two commercial DGGE systems, a C.B.S. Scientific DGGE-2001, and the Bio-Rad DCode system. In this context, identical nucleotide fragments exhibited differing migration behaviors depending on the model of apparatus utilized, with fragments denaturing at a lower gradient concentration and applied voltage on the Bio-Rad DCode system than on the C.B.S. Scientific DGGE-2001 system. Although equivalent PCR-DGGE profiles could be achieved with both brands of DGGE system, the composition of the denaturing gradient and application of electrophoresis time × voltage must be appropriately optimized to achieve congruent results across platforms.

  11. Organometallic Polymers. (United States)

    Carraher, Charles E., Jr.


    Reactions utilized to incorporate a metal-containing moiety into a polymer chain (addition, condensation, and coordination) are considered, emphasizing that these reactions also apply to smaller molecules. (JN)

  12. C1-inhibitor polymers activate the FXII-dependent kallikrein-kinin system

    DEFF Research Database (Denmark)

    Elenius Madsen, Daniel; Sidelmann, Johannes Jakobsen; Biltoft, Daniel


    attacks. HAE is caused by mutations in the C1-inh encoding gene, and we recently demonstrated that some mutations give rise to the presence of polymerized C1-inh in the plasma of HAE patients. METHODS: C1-inh polymers corresponding to the size of polymers observed in vivo were produced using heat...... denaturation and gel filtration. The ability of these polymers to facilitate FXII activation was assessed in vitro in an FXII activation bandshift assay. After spiking of plasma with C1-inh polymers, kallikrein generation was analyzed in a global kallikrein generation method. Prekallikrein consumption...... in the entire Danish HAE cohort was analyzed using an ELISA method. RESULTS: C1-inh polymers mediated FXII activation, and a dose dependent kallikrein generation in plasma spiked with C1-inh polymers. An increased (pre)kallikrein consumption was observed in plasma samples from HAE patients presenting with C1...

  13. Polymers All Around You! (United States)

    Gertz, Susan

    Background information on natural polymers, synthetic polymers, and the properties of polymers is presented as an introduction to this curriculum guide. Details are provided on the use of polymer products in consumer goods, polymer recycling, polymer densities, the making of a polymer such as GLUEP, polyvinyl alcohol, dissolving plastics, polymers…

  14. Interaction of ATP with acid-denatured cytochrome c via coupled folding-binding mechanism

    International Nuclear Information System (INIS)

    Ahluwalia, Unnati; Deep, Shashank


    Highlights: ► Interaction between ATP and cyt c takes place via coupled binding–folding mechanism. ► Binding of ATP to cyt c is endothermic. ► GTP and CTP induce similar level of helicity in acid-denatured cyt c as with ATP. ► Compactness induced by ATP is far greater than ADP or AMP. - Abstract: The non-native conformations of the cytochrome c (cyt c) are believed to play key roles in a number of physiological processes. Nucleotides are supposed to act as allosteric effectors in these processes by regulating structural transitions among different conformations of cyt c. To understand the interaction between acid denatured cytochrome c and nucleotides, spectroscopic and calorimetric techniques were utilized to observe the structural features of the induced conformation and the energetics of interaction of acid denatured cyt c with different nucleotides. Structure induction in the acid denatured cyt c was observed on the addition of the ∼1 mM nucleotide tri-phosphates (ATP/GTP/CTP) at 25 °C, however, not in the presence of 1 mM nucleotide mono and diphosphates. ATP-bound cyt c at pH 2.0 is likely to have a conformation that has intact α-helical domain. However, Met80-Fe(III) axial bond is still ruptured. Observed thermodynamics reflect interaction between nucleotide and cyt c via coupled binding–folding mechanism. DSC data suggest the preferential binding of the ATP to the folded conformation with respect to the acid denatured cyt c. ITC data indicate that the exothermic folding of cyt c was accompanied by endothermic binding of ATP to cyt c.

  15. Synchrotron radiation microtomography of Taylor bubbles in capillary two-phase flow

    International Nuclear Information System (INIS)

    Boden, Stephan; Santos Rolo, Tomy dos; Baumbach, Tilo; Hampel, Uwe


    We report on a study to measure the three-dimensional shape of Taylor bubbles in capillaries using synchrotron radiation in conjunction with ultrafast radiographic imaging. Moving Taylor bubbles in 2-mm round and square capillaries were radiographically scanned with an ultrahigh frame rate of up to 36,000 fps and 5.6-μm pixel separation. Consecutive images were properly processed to yield 2D transmission radiographs of high contrast-to-noise ratio. Application of 3D tomographic image reconstruction disclosed the 3D bubble shape. The results provide a reference data base for development of sophisticated interface resolving CFD computations. (orig.)

  16. Antimocrobial Polymer

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, William F. (Utica, OH); Huang, Zhi-Heng (Walnut Creek, CA); Wright, Stacy C. (Columbus, GA)


    A polymeric composition having antimicrobial properties and a process for rendering the surface of a substrate antimicrobial are disclosed. The composition comprises a crosslinked chemical combination of (i) a polymer having amino group-containing side chains along a backbone forming the polymer, (ii) an antimicrobial agent selected from quaternary ammonium compounds, gentian violet compounds, substituted or unsubstituted phenols, biguanide compounds, iodine compounds, and mixtures thereof, and (iii) a crosslinking agent containing functional groups capable of reacting with the amino groups. In one embodiment, the polymer is a polyamide formed from a maleic anhydride or maleic acid ester monomer and alkylamines thereby producing a polyamide having amino substituted alkyl chains on one side of the polyamide backbone; the crosslinking agent is a phosphine having the general formula (A)3P wherein A is hydroxyalkyl; and the antimicrobial agent is chlorhexidine, dimethylchlorophenol, cetyl pyridinium chloride, gentian violet, triclosan, thymol, iodine, and mixtures thereof.

  17. Polymer electronics

    CERN Document Server

    Geoghegan, Mark


    Polymer electronics is the science behind many important new developments in technology, such as the flexible electronic display (e-ink) and many new developments in transistor technology. Solar cells, light-emitting diodes, and transistors are all areas where plastic electronics is likely to, or is already having, a serious impact on our daily lives. With polymer transistors and light-emitting diodes now being commercialised, there is a clear need for a pedagogic text thatdiscusses the subject in a clear and concise fashion suitable for senior undergraduate and graduate students. The content


    Directory of Open Access Journals (Sweden)

    Md. Imtaiyaz Hassan


    Full Text Available Zinc α2-glycoprotein (ZAG and Prolactin induced protein (PIP are considered as important elements for fertility and biomarker for prostate and breast carcinomas. The stabilities of ZAG alone and its naturally occurring complex with PIP were compared. A significant difference in CD signal was recorded for native ZAG and ZAG-PIP complex against pH-, GdnHCl- and temperature-induced denaturation. These finding suggests that PIP plays a protective role for ZAG against several denaturants. PIP contributes to the hydrophobic as well as electrostatic interactions on ZAG for the complex formation. Moreover, the observed changes in far-UV spectra between ZAG and ZAG-PIP complex in the presence of PEG support the hydrophobic nature of the forces governing the formation of complex. This pH dependent study provides evidence that formation of the complex is a natural event required for physiological function.

  19. ZnO nanoparticles assist the refolding of denatured green fluorescent protein. (United States)

    Pandurangan, Muthuraman; Zamany, Ahmad Jawid; Kim, Doo Hwan


    Proteins are essential for cellular and biological processes. Proteins are synthesized and fold into the native structure to become active. The inability of a protein molecule to remain in its native conformation is called as protein misfolding, and this is due to several environmental factors. Protein misfolding and aggregation handle several human diseases. Protein misfolding is believed to be one of the causes of several disorders such as cancer, degenerative diseases, and metabolic pathologies. The zinc oxide (ZnO) nanoparticle was significantly promoted refolding of thermally denatured green fluorescent protein (GFP). In the present study, ZnO nanoparticles interaction with GFP was investigated by ultraviolet-visible spectrophotometer, fluorescence spectrophotometer, and dynamic light scattering. Results suggest that the ZnO nanoparticles significantly assist the refolding of denatured GFP. Copyright © 2015 John Wiley & Sons, Ltd.

  20. Differential denaturation of a crystalline Bence-Jones type cryoprotein as monitored by fluorescence. (United States)

    Finazzi Agrò, A; Crifò, C; Natali, P G; Chersi, A


    1) A Bence-Jones type protein (Cryo-Ver) showing the cold precipitation phenomenon has an extremely low intrinsic fluorescence when excited at 280-295 nm. 2) This fluorescence increases considerably upon denaturation of the molecule by heat or guanidine hydrochloride. Guanidine is about twice as effective as heat in terms of fluorescence yield. 3) The heat-denatured protein is still reactive with anti-cryoVer antibodies, at variance with the guanidine-treated samples. 4) Since the protein contains two tryptophans per mole, one in the constant portion of the molecule, the other in the variable region, it is proposed that heat treatment affects only the variable region, which seems involved in the cryoprecipitation phenomenon.

  1. Theoretical aspects of pressure and solute denaturation of proteins: A Kirkwood-buff-theory approach (United States)

    Ben-Naim, Arieh


    A new approach to the problem of pressure-denaturation (PD) and solute-denaturation (SD) of proteins is presented. The problem is formulated in terms of Le Chatelier principle, and a solution is sought in terms of the Kirkwood-Buff theory of solutions. It is found that both problems have one factor in common; the excluded volumes of the folded and the unfolded forms with respect to the solvent molecules. It is shown that solvent-induced effects operating on hydrophilic groups along the protein are probably the main reason for PD. On the other hand, the SD depends on the preferential solvation of the folded and the unfolded forms with respect to solvent and co-solvent molecules.

  2. Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Dufva, Martin; Hansen, Mikkel Fougt


    We present a microfluidic system and its use to measure DNA denaturation curves by varying the temperature or salt (Na+) concentration. The readout is based on real-time measurements of DNA hybridization using magnetoresistive sensors and magnetic nanoparticles (MNPs) as labels. We report the first...... melting curves of DNA hybrids measured as a function of continuously decreasing salt concentration at fixed temperature and compare them to the corresponding curves obtained vs. temperature at fixed salt concentration. The magnetoresistive sensor platform provided reliable results under varying....... The results demonstrate that concentration melting provides an attractive alternative to temperature melting in on-chip DNA denaturation experiments and further show that the magnetoresistive platform is attractive due to its low cross-sensitivity to temperature and liquid composition....

  3. Determination of the pK for the acid-induced denaturation of ferrocytochrome c. (United States)

    Varhac, Rastislav; Antalík, Marián


    Optical absorption spectroscopy was used to characterize the acid-induced conformational transition of horse heart ferrocytochrome c in the presence of urea. By using linear extrapolation to zero denaturant concentration, an apparent pK value for denaturation was found to be 0.86 +/- 0.07 at 25 degrees C. Visible absorption spectra in the presence of high urea concentration indicate that the dominant population is a high-spin, five-coordinate form under acidic conditions. Ferricytochrome c, used as a model reference system, shows a linear dependence of pK values versus urea concentration in the range from 0 to 4.1 M. Our data also indicate that even at a pH below 2 the iron-sulfur bond in ferrocytochrome c is present.

  4. In vitro refolding process of urea-denatured microbial transglutaminase without pro-peptide sequence. (United States)

    Yokoyama, Kei-ichi; Kunio, Ono; Ohtsuka, Tomoko; Nakamura, Nami; Seguro, Katsuya; Ejima, Daisuke


    Efficient refolding process of denatured mature microbial transglutaminase (MTG) without pro-peptide sequence was studied in the model system using urea-denatured pure MTG. Recombinant MTG, produced and purified to homogeneity according to the protocol previously reported, was denatured with 8M urea at neutral pH and rapidly diluted using various buffers. Rapid dilution with neutral pH buffers yielded low protein recovery. Reduction of protein concentration in the refolding solution did not improve protein recovery. Rapid dilution with alkaline buffers also yielded low protein recovery. However, dilution with mildly acidic buffers showed quantitative protein recovery with partial enzymatic activity, indicating that recovered protein was still arrested in the partially refolded state. Therefore, we further investigated the efficient refolding procedures of partially refolded MTG formed in the acidic buffers at low temperature (5 degrees C). Although enzymatic activity remained constant at pH 4, its hydrodynamic properties changed drastically during the 2h after the dilution. Titration of partially refolded MTG to pH 6 after 2h of incubation at pH 4.0 improved the enzymatic activity to a level comparable with that of the native enzyme. The same pH titration with incubation shorter than 2h yielded less enzymatic activity. Refolding trials performed at room temperature led to aggregation, with almost half of the activity yield obtained at 5 degrees C. We conclude that rapid dilution of urea denatured MTG under acidic pH at low temperature results in specific conformations that can then be converted to the native state by titration to physiological pH.

  5. Computer programs to assist in high resolution thermal denaturation and circular dichroism studies on nucleic acids (United States)

    Goodman, Thomas C.; Hardies, Stephen C.; Cortez, Carlos; Hillen, Wolfgang


    Computer programs are described that direct the collection, processing, and graphical display of numerical data obtained from high resolution thermal denaturation (1-3) and circular dichroism (4) studies. Besides these specific applications, the programs may also be useful, either directly or as programming models, in other types of spectrophotometric studies employing computers, programming languages, or instruments similar to those described here (see Materials and Methods). PMID:7335498

  6. Native and denatured bovine serum albumin. D.c. polarography, stripping voltammetry and constant current chronopotentiometry

    Czech Academy of Sciences Publication Activity Database

    Ostatná, Veronika; Uslu, B.; Dogan, B.; Ozkan, S.; Paleček, Emil


    Roč. 593, č. 1-2 (2006), s. 172-178 ISSN 0022-0728 R&D Projects: GA AV ČR(CZ) IAA500040513; GA MŠk(CZ) LC06035 Institutional research plan: CEZ:AV0Z50040507 Keywords : protein electrochemistry * bovine serum albumin * native and denatured proteins Subject RIV: BO - Biophysics Impact factor: 2.339, year: 2006

  7. Micro-CT imaging of denatured chitin by silver to explore honey bee and insect pathologies.

    Directory of Open Access Journals (Sweden)

    Peter R Butzloff

    Full Text Available BACKGROUND: Chitin and cuticle coatings are important to the environmental and immune defense of honey bees and insect pollinators. Pesticides or environmental effects may target the biochemistry of insect chitin and cuticle coating. Denaturing of chitin involves a combination of deacetylation, intercalation, oxidation, Schweiger-peeling, and the formation of amine hydrochloride salt. The term "denatured chitin" calls attention to structural and property changes to the internal membranes and external carapace of organisms so that some properties affecting biological activities are diminished. METHODOLOGY/PRINCIPAL FINDINGS: A case study was performed on honey bees using silver staining and microscopic computer-tomographic x-ray radiography (micro-CT. Silver nitrate formed counter-ion complexes with labile ammonium cations and reacted with amine hydrochloride. Silver was concentrated in the peritrophic membrane, on the abdomen, in the glossa, at intersegmental joints (tarsi, at wing attachments, and in tracheal air sacs. Imaged mono-esters and fatty acids from cuticle coating on external surfaces were apparently reduced by an alcohol pretreatment. CONCLUSIONS/SIGNIFICANCE: The technique provides 3-dimensional and sectional images of individual honey bees consistent with the chemistries of silver reaction and complex formation with denatured chitin. Environmental exposures and influences such as gaseous nitric oxide intercalant, trace oxidants such as ozone gas, oligosachharide salt conversion, exposure to acid rain, and chemical or biochemical denaturing by pesticides may be studied using this technique. Peritrophic membranes, which protect against food abrasion, microorganisms, and permit efficient digestion, were imaged. Apparent surface damage to the corneal lenses of compound eyes by dilute acid exposure consistent with chitin amine hydrochloride formation was imaged. The technique can contribute to existing insect pathology research, and may

  8. Confirmation of soybean plastid rRNAs by formaldehyde denaturing agarose gel electrophoresis. (United States)

    Zhu, Y Q; Zheng, Y; Chen, H B; Huang, L Q


    Owing to their prokaryotic origin, plastid rRNAs are mainly 23s/16s/5s rRNAs. We present a novel plant RNA isolation method in this paper. Also, not only the eukaryotic 28s (26s, 25s)/18s rRNAs but the prokaryotic 26s/23s rRNAs as well were demonstrated in a single sample for the first time by formaldehyde denaturing agarose gel electrophoresis.

  9. Equilibrium unfolding of A. niger RNase: pH dependence of chemical and thermal denaturation. (United States)

    Kumar, Gundampati Ravi; Sharma, Anurag; Kumari, Moni; Jagannadham, Medicherla V; Debnath, Mira


    Equilibrium unfolding of A. niger RNase with chemical denaturants, for example GuHCl and urea, and thermal unfolding have been studied as a function of pH using fluorescence, far-UV, near-UV, and absorbance spectroscopy. Because of their ability to affect electrostatic interactions, pH and chemical denaturants have a marked effect on the stability, structure, and function of many globular proteins. ANS binding studies have been conducted to enable understanding of the folding mechanism of the protein in the presence of the denaturants. Spectroscopic studies by absorbance, fluorescence, and circular dichroism and use of K2D software revealed that the enzyme has α + β type secondary structure with approximately 29% α-helix, 24% β-sheet, and 47% random coil. Under neutral conditions the enzyme is stable in urea whereas GuHCl-induced equilibrium unfolding was cooperative. A. niger RNase has little ANS binding even under neutral conditions. Multiple intermediates were populated during the pH-induced unfolding of A. niger RNase. Urea and temperature-induced unfolding of A. niger RNase into the molten globule-like state is non-cooperative, in contrast to the cooperativity seen with the native protein, suggesting the presence of two parts/domains, in the molecular structure of A. niger RNase, with different stability that unfolds in steps. Interestingly, the GuHCl-induced unfolding of the A state (molten globule state) of A. niger RNase is unique, because a low concentration of denaturant not only induces structural change but also facilitates transition from one molten globule like state (A(MG1)) into another (I(MG2)).

  10. Native and denatured forms of proteins can be discriminated at edge plane carbon electrodes

    Czech Academy of Sciences Publication Activity Database

    Ostatná, Veronika; Černocká, Hana; Kurzatkowska, K.; Paleček, Emil


    Roč. 735, JUL (2012), s. 31-36 ISSN 0003-2670 R&D Projects: GA AV ČR(CZ) KJB100040901; GA ČR(CZ) GAP301/11/2055; GA MŠk(CZ) ME09038 Institutional research plan: CEZ:AV0Z50040702 Keywords : protein denaturation * carbon electrodes * edge plane pyrolytic graphite Subject RIV: BO - Biophysics Impact factor: 4.387, year: 2012

  11. Multifocal peritoneal splenosis in Tc-99m-labeled heat-denatured red blood cell scintigraphy

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Min Ki; Hwang, Kyung Hoon; Choe, Won Sick [Gachon University Gil Medical Center, Incheon (Korea, Republic of)


    A 44-year-old man with a past medical history of splenectomy came to hospital because of epigastric pain abdominopelvic computed tomography(CT) showed a soft tissue mass and multifocal variable-sized nodules as well as finding suggestive of cholecystitis. Subsequently, he underwent Tc-99m-labeled heat- denatured red blood cell(RBC) scintigraphy to evaluate the mass and nodules. The scintigraphy confirmed multifocal peritoneal splenosis in the abdominopelvic cavity.

  12. Conducting Polymers

    Indian Academy of Sciences (India)

    backbone (by the process of doping) and make them electrically. Conducting Polymers. From a Laboratory Curiosity to the Market Place. S Ramakrishnan ..... switching occurs between transparent yellow and green in less than. 100ms. Thus, while these materials are yet to achieve the set target. (in terms of their life cycle) ...

  13. Conducting Polymers

    Indian Academy of Sciences (India)

    ized the plastics industry by providing a route to polypropylene. (Zeigler and Natta jointly won the. Nobel Prize in Chemistry in 1963 for their discovery.) ... transport of charge in these systems can be understood in a simple fashion, by causing the imine and amine nitrogens to exchange places along the polymer backbone (in ...

  14. Conducting Polymers

    Indian Academy of Sciences (India)

    the plastics industry by providing a route to polypropylene. (Zeigler and Natta jointly won the Nobel Prize in chemistry in 1963 for their discovery.) ... these systems can be understood in a simple fashion, by causing the imine and amine nitrogens to exchange places along the polymer backbone (in protonated emeraldinel.

  15. Conducting Polymers

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Conducting Polymers - From a Laboratory Curiosity to the Market Place. S Ramakrishnan. Volume 16 Issue 12 December 2011 pp 1254-1265. Fulltext. Click here to view fulltext PDF. Permanent link:

  16. Polymer solutions (United States)

    Krawczyk, Gerhard Erich [Bremen, DE; Miller, Kevin Michael [West Dundee, IL


    There is provided a method of making a polymer solution comprising polymerizing one or more monomer in a solvent, wherein said monomer comprises one or more ethylenically unsaturated monomer that is a multi-functional Michael donor, and wherein said solvent comprises 40% or more by weight, based on the weight of said solvent, one or more multi-functional Michael donor.

  17. Polymer physics

    CERN Document Server

    Gedde, Ulf W


    This book is the result of my teaching efforts during the last ten years at the Royal Institute of Technology. The purpose is to present the subject of polymer physics for undergraduate and graduate students, to focus the fundamental aspects of the subject and to show the link between experiments and theory. The intention is not to present a compilation of the currently available literature on the subject. Very few reference citations have thus been made. Each chapter has essentially the same structure: starling with an introduction, continuing with the actual subject, summarizing the chapter in 30D-500 words, and finally presenting problems and a list of relevant references for the reader. The solutions to the problems presented in Chapters 1-12 are given in Chapter 13. The theme of the book is essentially polymer science, with the exclusion of that part dealing directly with chemical reactions. The fundamentals in polymer science, including some basic polymer chemistry, are presented as an introduction in t...

  18. Supramolecular polymers

    National Research Council Canada - National Science Library

    Ciferri, A


    ... to the new class of self-assembled polymers that undergo reversible growth by the formation of noncovalent bonds. This class (Part II) is wider than expected: not only mainchain assemblies of hydrogen-bonded repeating units, but also planar organization of S-layer proteins, micellar and related three-dimensional structures of blo...

  19. Modified denatured lysozyme effectively solubilizes fullerene c60 nanoparticles in water (United States)

    Siepi, Marialuisa; Politi, Jane; Dardano, Principia; Amoresano, Angela; De Stefano, Luca; Monti, Daria Maria; Notomista, Eugenio


    Fullerenes, allotropic forms of carbon, have very interesting pharmacological effects and engineering applications. However, a very low solubility both in organic solvents and water hinders their use. Fullerene C60, the most studied among fullerenes, can be dissolved in water only in the form of nanoparticles of variable dimensions and limited stability. Here the effect on the production of C60 nanoparticles by a native and denatured hen egg white lysozyme, a highly basic protein, has been systematically studied. In order to obtain a denatured, yet soluble, lysozyme derivative, the four disulfides of the native protein were reduced and exposed cysteines were alkylated by 3-bromopropylamine, thus introducing eight additional positive charges. The C60 solubilizing properties of the modified denatured lysozyme proved to be superior to those of the native protein, allowing the preparation of biocompatible highly homogeneous and stable C60 nanoparticles using lower amounts of protein, as demonstrated by dynamic light scattering, transmission electron microscopy and atomic force microscopy studies. This lysozyme derivative could represent an effective tool for the solubilization of other carbon allotropes.

  20. The polysaccharides from porphyra yezoensis suppress the denaturation of bighead carp myofibrillar protein. (United States)

    Jiang, Long-Fa


    In this study, investigated was the effect of the porphyra yezoensis polysaccharides (PPs) on the denaturation of bighead carp (Aristichthys nobilis) myofibrillar protein (Mf) during frozen storage at -18°C for 90d. The PPs (2.5%, 5%, and 7.5%, respectively) was added to 100g of Mf. The changes in the Ca-adenylpyrophosphatase (ATPase) activity and unfrozen water content in Mf were examined to evaluate he denaturation of Mf during frozen storage. Ca-ATPase activity decreased gradually during frozen storage at -18°C upon addition of PPs. By contrast, Ca-ATPase activity in the control group dropped drastically during the first 45d of storage and then further decreased gradually for up to 90d of storage, indicating a biphasic denaturation pattern. PPs addition significantly increased sulfhydryl contents in the Mf of the treatment groups compared with that of the control group (p<0.05) during frozen storage at -18°C. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Effects of high pressure freezing (HPF) on denaturation of natural actomyosin extracted from prawn (Metapenaeus ensis). (United States)

    Cheng, Lina; Sun, Da-Wen; Zhu, Zhiwei; Zhang, Zhihang


    Effects of protein denaturation caused by high pressure freezing, involving Pressure-Factors (pressure, time) and Freezing-Factors (temperature, phase transition, recrystallization, ice crystal types), are complicated. In the current study, the conformation and functional changes of natural actomyosin (NAM) under pressure assisted freezing (PAF, 100,150,300,400,500MPa P -20°C/25min ), pressure shift freezing (PSF, 200MPa P -20°C/25min ), and immersion freezing ( 0.1MPa P -20°C/5min ) after pressure was released to 0.1MPa, as compared to normal immersion freezing process (IF, 0.1MPa P -20°C/30min ). Results indicated that PSF ( 200MPa P -20°C/30min ) could reduce the denaturation of frozen NAM and a pressure of 300MPa was the critical point to induce such a denaturation. During the periods of B→D in PSF or B→C→D in PAF, the generation and growth of ice crystals played an important role on changing the secondary and tertiary structure of the treated NAM. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Comparison of membrane electroporation and protein denature in response to pulsed electric field with different durations. (United States)

    Huang, Feiran; Fang, Zhihui; Mast, Jason; Chen, Wei


    In this paper, we compared the minimum potential differences in the electroporation of membrane lipid bilayers and the denaturation of membrane proteins in response to an intensive pulsed electric field with various pulse durations. Single skeletal muscle fibers were exposed to a pulsed external electric field. The field-induced changes in the membrane integrity (leakage current) and the Na channel currents were monitored to identify the minimum electric field needed to damage the membrane lipid bilayer and the membrane proteins, respectively. We found that in response to a relatively long pulsed electric shock (longer than the membrane intrinsic time constant), a lower membrane potential was needed to electroporate the cell membrane than for denaturing the membrane proteins, while for a short pulse a higher membrane potential was needed. In other words, phospholipid bilayers are more sensitive to the electric field than the membrane proteins for a long pulsed shock, while for a short pulse the proteins become more vulnerable. We can predict that for a short or ultrashort pulsed electric shock, the minimum membrane potential required to start to denature the protein functions in the cell plasma membrane is lower than that which starts to reduce the membrane integrity. Copyright © 2013 Wiley Periodicals, Inc.

  3. Remarkable activation of enzymes in nonaqueous media by denaturing organic cosolvents

    Energy Technology Data Exchange (ETDEWEB)

    Almarsson, O.; Klibanov, A.M. [Massachusetts Inst. of Tech., Cambridge, MA (United States). Dept. of Chemistry


    The rates of transesterification reactions catalyzed by the protease subtilisin Carlsberg suspended in various anhydrous solvents at 30 C can be increased more than 100-fold by the addition of denaturing organic cosolvents (dimethyl sulfoxide or formamide); in water, the same cosolvents exert no enzyme activation. At 4 C, the activation effect on the lyophilized protease is even higher, reaching 1,000-fold. Marked enhancement of enzymatic activity in anhydrous solvents by formamide is also observed for two other enzymes, {alpha}-chymotrypsin and Rhizomucor miehei lipase, and is manifested in two transesterification reactions. In addition to lyophilized subtilisin, crosslinked crystals of subtilisin are also amenable to the dramatic activation by the denaturing cosolvents. In contrast, subtilisin solubilized in anhydrous media by covalent modification with poly(ethylene glycol) exhibits only modest activation. These observations are rationalized in terms of a mechanistic hypothesis based on an enhanced protein flexibility in anhydrous milieu brought about by the denaturing organic cosolvents. The latter exert their lubricating effect largely at the interfaces between enzyme molecules in a solid preparation, thus easing the flexibility constraints imposed by protein-protein contacts.

  4. Denaturation of proteins by surfactants studied by the Taylor dispersion analysis.

    Directory of Open Access Journals (Sweden)

    Aldona Jelińska

    Full Text Available We showed that the Taylor Dispersion Analysis (TDA is a fast and easy to use method for the study of denaturation proteins. We applied TDA to study denaturation of β-lactoglobulin, transferrin, and human insulin by anionic surfactant sodium dodecyl sulfate (SDS. A series of measurements at constant protein concentration (for transferrin was 1.9 x 10-5 M, for β- lactoglobulin was 7.6 x 10-5 M, and for insulin was 1.2 x 10-4 M and varying SDS concentrations were carried out in the phosphate-buffered saline (PBS. The structural changes were analyzed based on the diffusion coefficients of the complexes formed at various surfactant concentrations. The concentration of surfactant was varied in the range from 1.2 x 10-4 M to 8.7 x 10-2 M. We determined the minimum concentration of the surfactant necessary to change the native conformation of the proteins. The minimal concentration of SDS for β-lactoglobulin and transferrin was 4.3 x 10-4 M and for insulin 2.3 x 10-4 M. To evaluate the TDA as a novel method for studying denaturation of proteins we also applied other methods i.e. electronic circular dichroism (ECD and dynamic light scattering (DLS to study the same phenomenon. The results obtained using these methods were in agreement with the results from TDA.

  5. Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding. (United States)

    Malhotra, Pooja; Jethva, Prashant N; Udgaonkar, Jayant B


    To characterize experimentally the ruggedness of the free energy landscape of protein folding is challenging, because the distributed small free energy barriers are usually dominated by one, or a few, large activation free energy barriers. This study delineates changes in the roughness of the free energy landscape by making use of the observation that a decrease in ruggedness is accompanied invariably by an increase in folding cooperativity. Hydrogen exchange (HX) coupled to mass spectrometry was used to detect transient sampling of local energy minima and the global unfolded state on the free energy landscape of the small protein single-chain monellin. Under native conditions, local noncooperative openings result in interconversions between Boltzmann-distributed intermediate states, populated on an extremely rugged "uphill" energy landscape. The cooperativity of these interconversions was increased by selectively destabilizing the native state via mutations, and further by the addition of a chemical denaturant. The perturbation of stability alone resulted in seven backbone amide sites exchanging cooperatively. The size of the cooperatively exchanging and/or unfolding unit did not depend on the extent of protein destabilization. Only upon the addition of a denaturant to a destabilized mutant variant did seven additional backbone amide sites exchange cooperatively. Segmentwise analysis of the HX kinetics of the mutant variants further confirmed that the observed increase in cooperativity was due to the smoothing of the ruggedness of the free energy landscape of folding of the protein by the chemical denaturant.

  6. Denaturation Kinetics of Whey Protein Isolate Solutions and Fouling Mass Distribution in a Plate Heat Exchanger

    Directory of Open Access Journals (Sweden)

    Marwa Khaldi


    Full Text Available Few investigations have attempted to connect the mechanism of dairy fouling to the chemical reaction of denaturation (unfolding and aggregation occurring in the bulk. The objective of this study is to contribute to this aspect in order to propose innovative controls to limit fouling deposit formation. Experimental investigations have been carried out to observe the relationship between the deposit mass distribution generated in plate heat exchangers (PHE by a whey protein isolate (WPI mainly composed of β-lactoglobulin (β-Lg and the ratio between the unfolding and aggregation rate constants. Experiments using a PHE were carried out at a pilot scale to identify the deposit distribution of a model fouling solution with different calcium contents. In parallel, laboratory experiments were performed to determine the unfolding/aggregation rate constants. Data analysis showed that (i β-Lg denaturation is highly dependent on the calcium content, (ii for each fouling solution, irrespective of the imposed temperature profile, the deposit mass in each channel and the ratio between the unfolding and aggregation rate constants seem to be well correlated. This study demonstrates that both the knowledge of the thermal profile and the β-Lg denaturation rate constants are required in order to predict accurately the deposit distribution along the PHE.

  7. Human hemoglobin denaturation as an alternative to the Draize test for predicting eye irritancy of surfactants. (United States)

    Mitjans, Montserrat; Infante, M Rosa; Vinardell, M Pilar


    Quantification of eye irritancy has been a problem for both the consumer product industry and ophthalmic researchers because of the need to predict the toxic potential of preparations that may come into contact with the ocular surface. The Draize rabbit eye test has been used for 60 years in attempts to predict human ocular irritancy based on topical instillation of the potential irritant and subjective scoring of ocular inflammation by direct visualization of the rabbit eye. The inadequacies of the Draize test have led to efforts in several laboratories to develop alternatives. We propose an alternative to the Draize eye irritation test, using human hemoglobin rather than bovine hemoglobin and studying the protein denaturation induced by potential irritants. Among the factors that affect eye irritation, protein denaturation has been reported as one of the most important factors that can result in corneal opacity. Human protein denaturation was measured as indicative of eye irritation. We studied different known irritant and non-irritant compounds to establish the predictability of the method. The compounds considered as irritants in vivo had the greatest effect in terms of decreased human hemoglobin absorbance. The proposed method is able to easily differentiate between irritant and non-irritants products in an easy manner. The method is easy, rapid, economical, and provides enough information about the potential eye irritant action of different surfactants.

  8. Isothermal chemical denaturation of large proteins: Path-dependence and irreversibility. (United States)

    Wafer, Lucas; Kloczewiak, Marek; Polleck, Sharon M; Luo, Yin


    State functions (e.g., ΔG) are path independent and quantitatively describe the equilibrium states of a thermodynamic system. Isothermal chemical denaturation (ICD) is often used to extrapolate state function parameters for protein unfolding in native buffer conditions. The approach is prudent when the unfolding/refolding processes are path independent and reversible, but may lead to erroneous results if the processes are not reversible. The reversibility was demonstrated in several early studies for smaller proteins, but was assumed in some reports for large proteins with complex structures. In this work, the unfolding/refolding of several proteins were systematically studied using an automated ICD instrument. It is shown that: (i) the apparent unfolding mechanism and conformational stability of large proteins can be denaturant-dependent, (ii) equilibration times for large proteins are non-trivial and may introduce significant error into calculations of ΔG, (iii) fluorescence emission spectroscopy may not correspond to other methods, such as circular dichroism, when used to measure protein unfolding, and (iv) irreversible unfolding and hysteresis can occur in the absence of aggregation. These results suggest that thorough confirmation of the state functions by, for example, performing refolding experiments or using additional denaturants, is needed when quantitatively studying the thermodynamics of protein unfolding using ICD. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA

    International Nuclear Information System (INIS)

    Fye, R.M.; Benham, C.J.


    Local denaturation, the separation at specific sites of the two strands comprising the DNA double helix, is one of the most fundamental processes in biology, required to allow the base sequence to be read both in DNA transcription and in replication. In living organisms this process can be mediated by enzymes which regulate the amount of superhelical stress imposed on the DNA. We present a numerically exact technique for analyzing a model of denaturation in superhelically stressed DNA. This approach is capable of predicting the locations and extents of transition in circular superhelical DNA molecules of kilobase lengths and specified base pair sequences. It can also be used for closed loops of DNA which are typically found in vivo to be kilobases long. The analytic method consists of an integration over the DNA twist degrees of freedom followed by the introduction of auxiliary variables to decouple the remaining degrees of freedom, which allows the use of the transfer matrix method. The algorithm implementing our technique requires O(N 2 ) operations and O(N) memory to analyze a DNA domain containing N base pairs. However, to analyze kilobase length DNA molecules it must be implemented in high precision floating point arithmetic. An accelerated algorithm is constructed by imposing an upper bound M on the number of base pairs that can simultaneously denature in a state. This accelerated algorithm requires O(MN) operations, and has an analytically bounded error. Sample calculations show that it achieves high accuracy (greater than 15 decimal digits) with relatively small values of M (M<0.05N) for kilobase length molecules under physiologically relevant conditions. Calculations are performed on the superhelical pBR322 DNA sequence to test the accuracy of the method. With no free parameters in the model, the locations and extents of local denaturation predicted by this analysis are in quantitatively precise agreement with in vitro experimental measurements

  10. Relationship between water-holding capacity and protein denaturation in broiler breast meat. (United States)

    Bowker, B; Zhuang, H


    The objective of this study was to determine the relationship between water-holding capacity (WHC) attributes and protein denaturation in broiler breast meat. Boneless skinless breast fillets (n = 72) were collected from a commercial processing plant at 2 h postmortem and segregated into low-WHC and high-WHC groups based on muscle pH and color (L*a*b*). At 6 and 24 h postmortem, brine uptake (%), cooking loss (%), and protein solubility (sarcoplasmic and myofibrillar) were measured and protein fractions were analyzed using SDS-PAGE. Drip loss accumulation (%) was measured after storage for 2 and 7 days postmortem. High-WHC fillets exhibited lower L*-lightness values and greater pH values at 2 and 24 h postmortem than low-WHC fillets. High-WHC fillets had greater brine uptake and less cooking loss at both 6 and 24 h postmortem compared to low-WHC fillets. Aging from 6 to 24 h postmortem increased brine uptake in high-WHC fillets, but did not affect cooking loss in either low-WHC or high-WHC fillets. Drip loss accumulation was greater in low-WHC fillets at both 2 and 7 days postmortem. Myofibrillar protein solubility decreased with postmortem time but was not different between low-WHC and high-WHC fillets. Sarcoplasmic protein solubility increased with postmortem time and was greater in high-WHC fillets. SDS-PAGE analysis indicated that low-WHC fillets exhibited more glycogen phosphorylase denaturation than high-WHC fillets as evidenced by a more extensive shift of the protein from the sarcoplasmic to the myofibrillar protein fraction. Correlation analysis revealed that overall protein solubility measurements were not related to WHC attributes but that the degree of glycogen phosphorylase denaturation was significantly correlated (|r| = 0.52 to 0.80) to measures of WHC. Data indicated that WHC differences in broiler breast fillets were not due to differences in myofibrillar protein denaturation and suggested that the denaturation of sarcoplasmic proteins onto

  11. Beneficial Effect of Sugar Osmolytes on the Refolding of Guanidine Hydrochloride-Denatured Trehalose-6-phosphate Hydrolase from Bacillus licheniformis

    Directory of Open Access Journals (Sweden)

    Jiau-Hua Chen


    Full Text Available The influence of three sugar osmolytes on the refolding of guanidine hydrochloride- (GdnHCl- denatured trehalose-6-phosphate hydrolase of Bacillus licheniformis (BlTreA was studied by circular dichroism (CD spectra, fluorescence emission spectra, and the recovery of enzymatic activity. These experimental results clearly indicated that sorbitol, sucrose, and trehalose at a concentration of 0.75 M improved the refolding yields of GdnHCl-denatured  BlTreA, probably due to the fact that these sugars favored the formation of tertiary architectures. Far-UV CD measurements demonstrated the ability of sugar osmolytes to shift the secondary structure of GdnHCl-denatured enzyme towards near-native conformations. ANS fluorescence intensity measurements revealed a reduction of exposed hydrophobic surfaces upon the treatment of denatured enzyme with sugar osmolytes. These observations suggest that sugar osmolytes possibly play a chaperone role in the refolding of chemically denatured BlTreA.

  12. Antibodies with specificity for native and denatured forms of ovalbumin differ in reactivity between enzyme-linked immunosorbent assays

    DEFF Research Database (Denmark)

    Holm, B.E.; Bergmann, A.C.; Hansen, Paul Robert


    constituting amino acids 130–135 and 136–141, respectively. Moreover, comparison of antibody reactivity to N OVA revealed that in the streptavidin-capture ELISA, antibody reactivity was notably reduced compared to ELISA employing surface-bound OVA. Collectively, immunization with native OVA preferentially...... to native OVA reacted strongly with native and denatured OVA in both assays, but did not react with the overlapping peptides. Polyclonal antibodies to denatured OVA reacted strongly with both OVA forms and with several of the overlapping peptides. Monoclonal antibodies to native OVA reacted preferentially...... with three-dimensional epitopes on native OVA and not with denatured OVA. Monoclonal antibodies to denatured OVA showed reactivity to both OVA forms. Two of these monoclonal antibodies, HYB 94-06 and 94-07, showed reactivity to overlapping peptides and their epitopes were identified as flexible structures...

  13. Comparison of the fine structure of mitochondrial DNA from Saccharomyces cerevisiae and S. carlsbergensis: electron microscopy of partially denatured molecules

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Christiansen, C


    Denaturation-maps of mitochondrial DNA from Saccharomyces cerevisiae and S. carlsbergensis have been derived from electron microscopic observations of partially denatured complete circular molecules and large fragments of these circles. The mitochondrial DNA from the two species differ by 6......% in total length, but seems from the maps to contain some regions of apparent close homology. The cleavage pattern of the two DNAs by the restriction endonuclease EcoRI is compared by gel electrophoresis....

  14. Non-Newtonian Mathematical Model and Numerical Simulations for the Blood Flow in Capillary Vessels

    Directory of Open Access Journals (Sweden)

    Balazs ALBERT


    Full Text Available In this paper, taking into consideration the rheological Cross type non-Newtonian model, we elaborate an axial-symmetric mathematical model for the blood flow in capillary vessel with adequate numeric algorithms. We take into account the elastic and porous behavior of the vessel wall which leads to a more realistic approach of the problem. We also accept that the change of substances through these vessels complies with the Starling hypothesis. This hypothesis states that the mass debit through the capillary wall is proportional to the pressure difference between outside and inside the capillaries. The existence of a slip condition along the permeable surface is also accepted using the results of Beavers and Joseph. The numerical experiments are made using COMSOL Multiphysics 3.3. Some numerical results with respect to the velocity field, pressure variation and the wall shear stress are presented.

  15. Application of Organic Monolithic Materials to Enantioseparation in Capillary Separation Techniques. (United States)

    Carrasco-Correa, Enrique Javier; Simo-Alfonso, Ernesto Francisco; Ramis-Ramos, Guillermo; Herero-Martinez, Jose Manuel


    This review article is primarily focused on the state-of-the-art of enantioseparations on organic monolithic materials. The article gives an overview of the chiral stationary phases and its application in capillary electrochromatography (CEC), and capillary- and nano-liquid chromatography (cLC and nLC). Since thousands of publications have been emerged from 2000's and citing all these papers would extend the scope of this review; then, recent developments from last 10 years (2006 to 2016) will be mentioned. Mostly, stationary phases based on copolymers obtained from chiral functional monomers and surface modifications of organic monoliths with chiral ligands will be discussed. The effective application of these chiral separation methodologies in several analysis areas will be also included. Copyright© Bentham Science Publishers; For any queries, please email at

  16. Imaging high-intensity focused ultrasound-induced tissue denaturation by multispectral photoacoustic method: an ex vivo study. (United States)

    Sun, Yao; O'Neill, Brian


    We present an ex vivo study for the first time, to the best of our knowledge, in multispectral photoacoustic imaging (PAI) of tissue denaturation induced by high-intensity focused ultrasound (HIFU) in this paper. Tissue of bovine muscle was thermally treated in a heated water bath and by HIFU, and then was imaged using a multispectral photoacoustic approach. Light at multiple optical wavelengths between 700 and 900 nm was delivered to the treated bovine muscle tissue to excite the photoacoustic signal. Apparent tissue denaturation has been observed in multispectral photoacoustic images after being treated in a water bath and by HIFU. It is interesting that the denaturation is more striking at shorter optical wavelength photoacoustic images than at longer optical wavelength photoacoustic images. Multispectral photoacoustic images of the tissue denaturation were further analyzed and the photoacoustic spectrums of the denaturized tissue were calculated in this paper. This study suggests that a multispectral PAI approach might be a promising tool to evaluate tissue denaturation induced by HIFU treatment.

  17. Antinociceptive and Anti-Inflammatory Effects of Orally Administrated Denatured Naja Naja Atra Venom on Murine Rheumatoid Arthritis Models

    Directory of Open Access Journals (Sweden)

    Kou-Zhu Zhu


    Full Text Available To investigate the antinociceptive and anti-inflammatory activities of the denatured Naja Naja atra venom (NNAV in rheumatoid arthritis-associated models, the denatured NNAV (heat treated; 30, 90, 270 μg/kg, the native NNAV (untreated with heat; 90 μg/kg, and Tripterygium wilfordii polyglycoside (TWP, 15 mg/kg were administrated orally either prophylactically or therapeutically. We measured time of licking the affected paw in formaldehyde-induced inflammatory model, paw volume in egg-white-induced inflammation, and granuloma weight in formalin-soaked filter paper-induced granuloma. For adjuvant-induced arthritis (AIA rats, paw edema, mechanical withdrawal threshold, serum levels of TNF-α and IL-10, and histopathological changes of the affected paw were assessed. We found that the denatured NNAV (90, 270 μg/kg significantly reduced time of licking paw, paw volume, and granuloma weight in above inflammatory models and also attenuated paw edema, mechanical hyperalgesia, and histopathology changes in AIA rats. Additionally, the increase in serum TNF-α and the decrease in serum IL-10 in AIA rats were reversed by the denatured NNAV. Although the native NNAV and TWP rendered the similar pharmacological actions on the above four models with less potency than that of the denatured NNAV, these findings demonstrate that oral administration of the denatured NNAV produces antinociceptive and anti-inflammatory activities on rheumatoid arthritis.

  18. Fluctuating partially native-like topologies in the acid denatured ensemble of autolysis resistant HIV-1 protease. (United States)

    Rout, Manoj Kumar; Hosur, Ramakrishna V


    Folding, in-vivo, starts from a denatured state and thus the nature of the denatured state would play an important role in directing the folding of a protein. We report here NMR characterization of the acid-denatured state of a mutant of HIV-1 protease, designed to prevent autolysis (Q7K, L33I, L63I) and to prevent cysteine oxidation (C67A and C95A). Secondary chemical shifts, TALOS analysis of chemical shifts and (15)N relaxation data (R(1), R(2), NOE) coupled with AABUF and hydrophobicity calculations, suggest formation of hydrophobic clusters and possibility of some partially native-like topologies in the acid denatured state of the protease. The structural and dynamics characteristics of the acid denatured PR seem to be considerably different from those of the guanidine or urea denatured states of some variants of PR. These would have implications for the folding and auto-processing of the enzyme in-vivo.

  19. Polymer blends

    Energy Technology Data Exchange (ETDEWEB)

    Allen, Scott D.; Naik, Sanjeev


    The present invention provides, among other things, extruded blends of aliphatic polycarbonates and polyolefins. In one aspect, provided blends comprise aliphatic polycarbonates such as poly(propylene carbonate) and a lesser amount of a crystalline or semicrystalline polymer. In certain embodiments, provided blends are characterized in that they exhibit unexpected improvements in their elongation properties. In another aspect, the invention provides methods of making such materials and applications of the materials in applications such as the manufacture of consumer packaging materials.

  20. Influence of the electrokinetic injection conditions on the separation of DNA fragments in capillary electrophoresis


    Catai Jonatan Ricardo; Carrilho Emanuel


    In genetic analysis by capillary electrophoresis with polymer solutions there are many variables that affect separation of the DNA fragments. A very critical one is the sample injection process, which can considerably affect the peak efficiency and the resolution. In this work, we have studied the influence of the DNA sample composition and the electrokinetic injection conditions in the separation of DNA fragments by capillary electrophoresis using replaceable polymer solutions. The studies w...

  1. A Theoretical Analysis of the Influence of Electroosmosis on the Effective Ionic Mobility in Capillary Zone Electrophoresis (United States)

    Hijnen, Hens


    A theoretical description of the influence of electroosmosis on the effective mobility of simple ions in capillary zone electrophoresis is presented. The mathematical equations derived from the space-charge model contain the pK[subscript a] value and the density of the weak acid surface groups as parameters characterizing the capillary. It is…

  2. Patterning titania with conventional and modified micromolding in capillaries technique from sol-gel and dispersion solutions

    NARCIS (Netherlands)

    Khan, Sajid; ten Elshof, Johan E.


    We report TiO2 patterns obtained by a soft-lithographic technique called 'micromolding in capillaries' using sol¿gel and dispersion solutions. A comparison between patterning with a sol¿gel and dispersion solutions has been performed. The patterns obtained from sol¿gel solutions showed good adhesion

  3. Solid state stability of proteins III: calorimetric (DSC) and spectroscopic (FTIR) characterization of thermal denaturation in freeze dried human growth hormone (hGH). (United States)

    Pikal, Michael J; Rigsbee, Daniel; Roy, Michael L


    This research is a study of the changes in secondary structure (Fourier transform infrared spectroscopy, FTIR), aggregation, and loss of the magnitude of the heat of denaturation upon scanning to and partially through the temperature range of the thermal denaturation peak of a model protein, human growth hormone (hGH). We study two formulations, a system of essentially pure protein (with a trace of phosphate buffer) and a system formulated with trehalose in a 3:1 trehalose:hGH weight ratio. The extent of denaturation is measured by loss of secondary structure by FTIR, the loss of heat of denaturation by differential scanning calorimetry (DSC), and the fraction of protein aggregated by HPLC. We examine loss of structure on heating to the DSC onset of thermal denaturation and restoration of structure by cooling below the denaturation temperature and holding to (nominally) allow time for refolding, and we also examine restoration of structure upon dissolving and refreeze drying samples heated to selected temperatures in the denaturation range. We find that denaturation occurs only above the glass transition temperature, is highly cooperative, and is only reversible by redissolving the "denatured" formulated (trehalose) solid. Further, all measures of the extent of denaturation are in essential agreement.

  4. Single Molecular Level Probing of Structure and Dynamics of Papain Under Denaturation. (United States)

    Sengupta, Bhaswati; Chaudhury, Apala; Das, Nilimesh; Sen, Pratik


    Papain is a cysteine protease enzyme present in papaya and known to help in digesting peptide. Thus the structure and function of the active site of papain is of interest. The objective of present study is to unveil the overall structural transformation and the local structural change around the active site of papain as a function of chemical denaturant. Papain has been tagged at Cys-25 with a thiol specific fluorescence probe N-(7- dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA). Guanidine hydrochloride (GnHCl) has been used as the chemical denaturant. Steady state, time-resolved, and single molecular level fluorescence techniques was applied to map the change in the local environment. It is found that papain undergoes a two-step denaturation in the presence of GnHCl. Fluorescence correlation spectroscopic (FCS) data indicate that the size (hydrodynamic diameter) of native papain is ~36.8 Å, which steadily increases to ~53 Å in the presence of 6M GnHCl. FCS study also reveals that the conformational fluctuation time of papain is 6.3 µs in its native state, which decreased to 2.7 µs in the presence of 0.75 M GnHCl. Upon further increase in GnHCl concentration the conformational fluctuation time increase monotonically till 6 M GnHCl, where the time constant is measured as 14 µs. On the other hand, the measurement of ellipticity, hence the helical structure, by circular dichroism spectroscopy is found to be incapable to capture such structural transformation. It is concluded that in the presence of small amount of GnHCl the active site of papain takes up a more compact structure (although the overall size increases) than in the native state, which has been designated as the intermediate state. Copyright© Bentham Science Publishers; For any queries, please email at

  5. Helical Propensity Affects the Conformational Properties of the Denatured State of Cytochrome c'. (United States)

    Danielson, Travis A; Bowler, Bruce E


    Changing the helical propensity of a polypeptide sequence might be expected to affect the conformational properties of the denatured state of a protein. To test this hypothesis, alanines at positions 83 and 87 near the center of helix 3 of cytochrome c' from Rhodopseudomonas palustris were mutated to serine to decrease the stability of this helix. A set of 13 single histidine variants in the A83S/A87S background were prepared to permit assessment of the conformational properties of the denatured state using histidine-loop formation in 3 M guanidine hydrochloride. The data are compared with previous histidine-heme loop formation data for wild-type cytochrome c'. As expected, destabilization of helix 3 decreases the global stabilities of the histidine variants in the A83S/A87S background relative to the wild-type background. Loop stability versus loop size data yields a scaling exponent of 2.1 ± 0.2, similar to the value of 2.3 ± 0.2 obtained for wild-type cytochrome c'. However, the stabilities of all histidine-heme loops, which contain the helix 3 sequence segment, are increased in the A83S/A87S background compared to the wild-type background. Rate constants for histidine-heme loop breakage are similar for the wild-type and A83S/A87S variants. However, for histidine-heme loops that contain the helix 3 sequence segment, the rate constants for loop formation increase in the A83S/A87S background compared to the wild-type background. Thus, residual helical structure appears to stiffen the polypeptide chain slowing loop formation in the denatured state. The implications of these results for protein folding mechanisms are discussed. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  6. Stabilizing effect of biochar on soil extracellular enzymes after a denaturing stress. (United States)

    Elzobair, Khalid A; Stromberger, Mary E; Ippolito, James A


    Stabilizing extracellular enzymes may maintain enzymatic activity while protecting enzymes from proteolysis and denaturation. A study determined whether a fast pyrolysis hardwood biochar (CQuest™) would reduce evaporative losses, subsequently stabilizing soil extracellular enzymes and prohibiting potential enzymatic activity loss following a denaturing stress (microwaving). Soil was incubated in the presence of biochar (0%, 1%, 2%, 5%, or 10% by wt.) for 36 days and then exposed to microwave energies (0, 400, 800, 1600, or 3200 J g(-1) soil). Soil enzymes (β-glucosidase, β-d-cellobiosidase, N-acetyl-β-glucosaminidase, phosphatase, leucine aminopeptidase, β-xylosidase) were analyzed by fluorescence-based assays. Biochar amendment reduced leucine aminopeptidase and β-xylosidase potential activity after the incubation period and prior to stress exposure. The 10% biochar rate reduced soil water loss at the lowest stress level (400 J microwave energy g(-1) soil). Enzyme stabilization was demonstrated for β-xylosidase; intermediate biochar application rates prevented a complete loss of this enzyme's potential activity after soil was exposed to 400 (1% biochar treatment) or 1600 (5% biochar treatment) J microwave energy g(-1) soil. Remaining enzyme potential activities were not affected by biochar, and activities decreased with increasing stress levels. We concluded that biochar has the potential to reduce evaporative soil water losses and stabilize certain extracellular enzymes where activity is maintained after a denaturing stress; this effect was biochar rate and enzyme dependent. While biochar may reduce the potential activity of certain soil extracellular enzymes, this phenomenon was not universal as the majority of enzymes assayed in this study were unaffected by exposure to biochar. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Mechanisms of amphipathic helical peptide denaturation by guanidinium chloride and urea: a molecular dynamics simulation study (United States)

    Mehrnejad, Faramarz; Khadem-Maaref, Mahmoud; Ghahremanpour, Mohammad Mehdi; Doustdar, Farahnoosh


    Urea and GdmCl are widely used to denature proteins at high concentrations. Here, we used MD simulations to study the denaturation mechanisms of helical peptide in different concentrations of GdmCl and urea. It was found that the helical structure of the peptide in water simulation is disappeared after 5 ns while the helicity of the peptide is disappeared after 70 ns in 2 M urea and 25 ns in 1 M GdmCl. Surprisingly, this result shows that the helical structure in low concentration of denaturants is remained more with respect to that solvated in water. The present work strongly suggests that urea interact more preferentially to non-polar and aromatic side chains in 2 M urea; therefore, hydrophobic residues are in more favorable environment in 2 M urea. Our results also reveal that the hydrogen bonds between urea and the backbone is the dominant mechanism by which the peptide is destabilized in high concentration of urea. In 1 M and 2 M GdmCl, GdmCl molecules tend to engage in transient stacking interactions with aromatics and hydrophobic planar side chains that lead to displacement of water from the hydration surface, providing more favorable environment for them. This shows that accumulation of GdmCl around hydrophobic surfaces in 1 M and 2 M GdmCl solutions prevents proper solvation of the peptide at the beginning. In high GdmCl concentrations, water solvate the peptide better than 1 M and 2 M GdmCl. Therefore, our results strongly suggest that hydrogen bonds between water and the peptide are important factors in the destabilization of peptide in GdmCl solutions.

  8. A study of the thermal denaturation of the S-layer protein from Lactobacillus salivarius (United States)

    Lighezan, Liliana; Georgieva, Ralitsa; Neagu, Adrian


    Surface layer (S-layer) proteins display an intrinsic self-assembly property, forming monomolecular crystalline arrays, identified in outermost structures of the cell envelope in many organisms, such as bacteria and archaea. Isolated S-layer proteins also possess the ability to recrystallize into regular lattices, being used in biotechnological applications, such as controlling the architecture of biomimetic surfaces. To this end, the stability of the S-layer proteins under high-temperature conditions is very important. In this study, the S-layer protein has been isolated from Lactobacillus salivarius 16 strain of human origin, and purified by cation-exchange chromatography. Using circular dichroism (CD) spectroscopy, we have investigated the thermal denaturation of the S-layer protein. The far- and near-UV CD spectra have been collected, and the temperature dependence of the CD signal in these spectral domains has been analyzed. The variable temperature results show that the secondary and tertiary structures of the S-layer protein change irreversibly due to the heating of the sample. After the cooling of the heated protein, the secondary and tertiary structures are partially recovered. The denaturation curves show that the protein unfolding depends on the sample concentration and on the heating rate. The secondary and tertiary structures of the protein suffer changes in the same temperature range. We have also detected an intermediate state in the protein denaturation pathway. Our results on the thermal behavior of the S-layer protein may be important for the use of S-layer proteins in biotechnological applications, as well as for a better understanding of the structure and function of S-layer proteins.

  9. Denaturing high-performance liquid chromatography mutation analysis in patients with reduced Protein S levels

    DEFF Research Database (Denmark)

    Bathum, Lise; Münster, Anna-Marie; Nybo, Mads


    diagnosis and risk estimation. The aim was to design a high-throughput genetic analysis based on denaturing high-performance liquid chromatography to identify sequence variations in the gene coding for Protein S. PATIENTS: In total, 55 patients referred to the Section of Thrombosis and Haemostasis, Odense......BACKGROUND: Patients with congenital Protein S deficiency have increased risk of venous thromboembolism. However, Protein S levels show large intra-individual variation and the biochemical assays have low accuracy and a high interlaboratory variability. Genetic analysis might aid in a more precise......, giving a precise diagnosis and subsequently a better risk estimation....

  10. Denaturation of collagen structures and their transformation under the physical and chemical effects (United States)

    Ivankin, A.; Boldirev, V.; Fadeev, G.; Baburina, M.; Kulikovskii, A.; Vostrikova, N.


    The process of denaturation of collagen structures under the influence of physical and chemical factors play an important role in the manufacture of food technology and the production of drugs for medicine and cosmetology. The paper discussed the problem of the combined effects of heat treatment, mechanical dispersion and ultrasonic action on the structural changes of the animal collagen in the presence of weak protonated organic acids. Algorithm combined effects of physical and chemical factors as a result of the formation of the technological properties of products containing collagen has been shown.

  11. Native, denatured and reduced BSA enhancement of chronopotentiometric peak H by guanidinium chloride

    Czech Academy of Sciences Publication Activity Database

    Ostatná, Veronika; Paleček, Emil


    Roč. 53, č. 11 (2008), s. 4014-4021 ISSN 0013-4686 R&D Projects: GA ČR(CZ) GA301/07/0490; GA ČR(CZ) GP202/07/P497; GA AV ČR(CZ) IAA500040513; GA MŠk(CZ) LC06035 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : constant current chronopotentiometry * protein denaturation * guanidinium chloride Subject RIV: AQ - Safety, Health Protection, Human - Machine Impact factor: 3.078, year: 2008

  12. Screening for mutations in the uroporphyrinogen decarboxylase gene using denaturing gradient gel electrophoresis

    DEFF Research Database (Denmark)

    Christiansen, L; Ged, C; Hombrados, I


    , confirming the heterogeneity of the underlying genetic defects of these diseases. We have established a denaturing gradient gel electrophoresis (DGGE) assay for mutation detection in the UROD gene, enabling the simultaneous screening for known and unknown mutations. The established assay has proved able...... to exon skipping, and a 2-bp deletion (415-416delTA) resulting in a frameshift and the introduction of a premature stop codon. Heterologous expression and enzymatic studies of the mutant proteins demonstrate that the three mutations leading to shortening or truncation of the UROD protein have no residual...

  13. Effect of heating strategies on whey protein denaturation--Revisited by liquid chromatography quadrupole time-of-flight mass spectrometry. (United States)

    Akkerman, M; Rauh, V M; Christensen, M; Johansen, L B; Hammershøj, M; Larsen, L B


    Previous standards in the area of effect of heat treatment processes on milk protein denaturation were based primarily on laboratory-scale analysis and determination of denaturation degrees by, for example, electrophoresis. In this study, whey protein denaturation was revisited by pilot-scale heating strategies and liquid chromatography quadrupole time-of-flight mass spectrometer (LC/MC Q-TOF) analysis. Skim milk was heat treated by the use of 3 heating strategies, namely plate heat exchanger (PHE), tubular heat exchanger (THE), and direct steam injection (DSI), under various heating temperatures (T) and holding times. The effect of heating strategy on the degree of denaturation of β-lactoglobulin and α-lactalbumin was determined using LC/MC Q-TOF of pH 4.5-soluble whey proteins. Furthermore, effect of heating strategy on the rennet-induced coagulation properties was studied by oscillatory rheometry. In addition, rennet-induced coagulation of heat-treated micellar casein concentrate subjected to PHE was studied. For skim milk, the whey protein denaturation increased significantly as T and holding time increased, regardless of heating method. High denaturation degrees were obtained for T >100°C using PHE and THE, whereas DSI resulted in significantly lower denaturation degrees, compared with PHE and THE. Rennet coagulation properties were impaired by increased T and holding time regardless of heating method, although DSI resulted in less impairment compared with PHE and THE. No significant difference was found between THE and PHE for effect on rennet coagulation time, whereas the curd firming rate was significantly larger for THE compared with PHE. Micellar casein concentrate possessed improved rennet coagulation properties compared with skim milk receiving equal heat treatment. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  14. Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation. (United States)

    Mikulecky, Peter J; Feig, Andrew L


    In proteins, empirical correlations have shown that changes in heat capacity (DeltaC(P)) scale linearly with the hydrophobic surface area buried upon folding. The influence of DeltaC(P) on RNA folding has been widely overlooked and is poorly understood. In addition to considerations of solvent reorganization, electrostatic effects might contribute to DeltaC(P)s of folding in polyanionic species such as RNAs. Here, we employ a perturbation method based on electrostatic theory to probe the hot and cold denaturation behavior of the hammerhead ribozyme. This treatment avoids much of the error associated with imposing two-state folding models on non-two-state systems. Ribozyme stability is perturbed across a matrix of solvent conditions by varying the concentration of NaCl and methanol co-solvent. Temperature-dependent unfolding is then monitored by circular dichroism spectroscopy. The resulting array of unfolding transitions can be used to calculate a DeltaC(P) of folding that accurately predicts the observed cold denaturation temperature. We confirm the accuracy of the calculated DeltaC(P) by using isothermal titration calorimetry, and also demonstrate a methanol-dependence of the DeltaC(P). We weigh the strengths and limitations of this method for determining DeltaC(P) values. Finally, we discuss the data in light of the physical origins of the DeltaC(P)s for RNA folding and consider their impact on biological function.

  15. Approach to analysis of single nucleotide polymorphisms by automated constant denaturant capillary electrophoresis

    International Nuclear Information System (INIS)

    Bjoerheim, Jens; Abrahamsen, Torveig Weum; Kristensen, Annette Torgunrud; Gaudernack, Gustav; Ekstroem, Per O.


    Melting gel techniques have proven to be amenable and powerful tools in point mutation and single nucleotide polymorphism (SNP) analysis. With the introduction of commercially available capillary electrophoresis instruments, a partly automated platform for denaturant capillary electrophoresis with potential for routine screening of selected target sequences has been established. The aim of this article is to demonstrate the use of automated constant denaturant capillary electrophoresis (ACDCE) in single nucleotide polymorphism analysis of various target sequences. Optimal analysis conditions for different single nucleotide polymorphisms on ACDCE are evaluated with the Poland algorithm. Laboratory procedures include only PCR and electrophoresis. For direct genotyping of individual SNPs, the samples are analyzed with an internal standard and the alleles are identified by co-migration of sample and standard peaks. In conclusion, SNPs suitable for melting gel analysis based on theoretical thermodynamics were separated by ACDCE under appropriate conditions. With this instrumentation (ABI 310 Genetic Analyzer), 48 samples could be analyzed without any intervention. Several institutions have capillary instrumentation in-house, thus making this SNP analysis method accessible to large groups of researchers without any need for instrument modification

  16. Conceptual design characteristics of a denatured molten-salt reactor with once-through fueling

    Energy Technology Data Exchange (ETDEWEB)

    Engel, J.R.; Bauman, H.F.; Dearing, J.F.; Grimes, W.R.; McCoy, H.E.; Rhoades, W.A.


    A study was made to examine the conceptual feasibility of a molten-salt power reactor fueled with denatured /sup 235/U and operated with a minimum of chemical processing. Because such a reactor would not have a positive breeding gain, reductions in the fuel conversion ratio were allowed in the design to achieve other potentially favorable characteristics for the reactor. A conceptual core design was developed in which the power density was low enough to allow a 30-year life expectancy of the moderator graphite with a fluence limit of 3 x 10/sup 26/ neutrons/m/sup 2/ (E > 50 keV). This reactor could be made critical with about 3450 kg of 20% enriched /sup 235/U and operated for 30 years with routine additions of denatured /sup 235/U and no chemical processing for removal of fission products. A review of the chemical considerations assoicated with the conceptual fuel cycle indicates that no substantial difficulties would be expected if the soluble fission products and higher actinides were allowed to remain in the fuel salt for the life of the plant.

  17. Effects of thermally induced denaturation on technological-functional properties of whey protein isolate-based films. (United States)

    Schmid, M; Krimmel, B; Grupa, U; Noller, K


    This study examined how and to what extent the degree of denaturation affected the technological-functional properties of whey protein isolate (WPI)-based coatings. It was observed that denaturation affected the material properties of WPI-coated films significantly. Surface energy decreased by approximately 20% compared with native coatings. Because the surface energy of a coating should be lower than that of the substrate, this might result in enhanced wettability characteristics between WPI-based solution and substrate surface. Water vapor barrier properties increased by about 35% and oxygen barrier properties increased by approximately 33%. However, significant differences were mainly observed between coatings made of fully native WPI and ones with a degree of denaturation of 25%. Higher degrees of denaturation did not lead to further improvement of material properties. This observation offers cost-saving potential: a major share of denatured whey proteins may be replaced by fully native ones that are not exposed to energy-intensive heat treatment. Furthermore, native WPI solutions can be produced with higher dry matter content without gelatinizing. Hence, less moisture has to be removed through drying, resulting in reduced energy consumption. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  18. Development of a non-toxic and non-denaturing formulation process for encapsulation of SDF-1α into PLGA/PEG-PLGA nanoparticles to achieve sustained release. (United States)

    Haji Mansor, Muhammad; Najberg, Mathie; Contini, Aurélien; Alvarez-Lorenzo, Carmen; Garcion, Emmanuel; Jérôme, Christine; Boury, Frank


    Chemokines are known to stimulate directed migration of cancer cells. Therefore, the strategy involving gradual chemokine release from polymeric vehicles for trapping cancer cells is of interest. In this work, the chemokine stromal cell-derived factor-1α (SDF-1α) was encapsulated into nanoparticles composed of poly-(lactic-co-glycolic acid) (PLGA) and a polyethylene glycol (PEG)-PLGA co-polymer to achieve sustained release. SDF-1α, and lysozyme as a model protein, were firstly precipitated to promote their stability upon encapsulation. A novel phase separation method utilising a non-toxic solvent in the form of isosorbide dimethyl ether was developed for the individual encapsulation of SDF-1α and lysozyme precipitates. Uniform nanoparticles of 200-250 nm in size with spherical morphologies were successfully synthesised under mild formulation conditions and conveniently freeze-dried in the presence of hydroxypropyl-β-cyclodextrin as a stabiliser. The effect of PLGA carboxylic acid terminal capping on protein encapsulation efficiency and release rate was also explored. Following optimisation, sustained release of SDF-1α was achieved over a period of 72 h. Importantly, the novel encapsulation process was found to induce negligible protein denaturation. The obtained SDF-1α nanocarriers may be subsequently incorporated within a hydrogel or other scaffolds to establish a chemokine concentration gradient for the trapping of glioblastoma cells. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Properties of the microcirculation in capillary bundles of rat spinotrapezius muscle fascia (United States)

    Jacobitz, Frank; Engebrecht, Cheryn; Metzger, Ian; Porterfield, Colin


    Properties of the microcirculation in capillary bundles of rat spinotrapezius muscle fascia are investigated using microscope observations, empirical modeling, and numerical simulations. Capillary bundles consist of a network of feeding arterioles, draining venules, and capillary vessels. A dozen samples of muscle fascia tissue were prepared for microscope observation. The chosen method of preparation allows for the long-term preservation of the tissue samples for future studies. Capillary bundles are photographed under a microscope with 40x magnification. From the images, the microvasculature of the tissue samples is reconstructed. It was found, for example, that the distribution of vessel length in a capillary bundle follows a log-normal law. In addition to a statistical analysis of the vessel data, the network topology is used for numerical simulations of the flow in the capillary bundles. The numerical approach uses a sparse-matrix solver and it considers vessel elasticity and blood rheology. The numerical simulations show, for example, a strong pressure drop across the capillary vessels of the bundle.

  20. In-capillary self-assembly and proteolytic cleavage of polyhistidine peptide capped quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jianhao; Li, Jingyan; Li, Jinchen; Liu, Feifei [School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, 213164 (China); Zhou, Xiang; Yao, Yi [Changzhou Qianhong Bio-pharma Co. Ltd, Changzhou 213164, Jiangsu (China); Wang, Cheli [School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, 213164 (China); Qiu, Lin, E-mail: [School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, 213164 (China); Jiang, Pengju, E-mail: [School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, 213164 (China); State Key Laboratory of Pharmaceutical Biotechnology, Nanjing, Jiangsu (China)


    A new method using fluorescence coupled capillary electrophoresis (CE-FL) for monitoring self-assembly and proteolytic cleavage of hexahistidine peptide capped quantum dots (QDs) inside a capillary has been developed in this report. QDs and the ATTO 590-labeled hexahistidine peptide (H6-ATTO) were injected into a capillary, sequentially. Their self-assembly inside the capillary was driven by a metal-affinity force which yielded a new fluorescence signal due to Förster resonance energy transfer (FRET). The highly efficient separation of fluorescent complexes and the FRET process were analyzed using CE-FL. The self-assembly of QDs and biomolecules was found to effectively take place inside the capillary. The kinetics of the assembly was monitored by CE-FL, and the approach was extended to the study of proteolytic cleavage of surface conjugated peptides. Being the first in-depth analysis of in-capillary nanoparticle–biomolecule assembly, the novel approach reported here provides inspiration to the development of QD-based FRET probes for biomedical applications. - Highlights: • We examined the self-assembly QDs with H6-ATTO inside a capillary. • We prove CE-FL to be a powerful method to resolve QDs-H6-ATTO complex. • We achieve chromatographic separation of QDs-H6-ATTO complex. • We discovered a novel strategy for the online detection of thrombin. • This technique integrated “injection, mixing, reaction, separation and detection”.

  1. Selectivity in capillary electrophoresis:  application to chiral separations with cyclodextrins. (United States)

    Lelièvre, F; Gareil, P; Jardy, A


    In order to accurately evaluate the performances of any electrolyte medium, a clear concept of selectivity in capillary electrophoresis and related electroseparation techniques is proposed. Selectivity is defined as the ratio of the affinity factors of both analytes for a separating agent (phase, pseudophase, or complexing agent present in the background electrolyte). When in the presence of a complexing agent and if only 1:1 complexation occurs, selectivity corresponds to the ratio of the apparent binding constants and is independent of the concentration of the complexing agent. This concept is illustrated through the separations of neutral and anionic enantiomers in the presence of a cationic cyclodextrin, the mono(6-amino-6-deoxy)-β-cyclodextrin, as a chiral complexing agent. The values obtained for different pairs of enantiomers are discussed with regard to the functional groups that distinguish them. When the analytes have the same mobilities in free solution and in their complexed form, then the resolution equation developed in micellar electrokinetic chromatography may be applied and optimum conditions (affinity factors, chiral agent concentration) can be predicted.

  2. Flow rate dependent extra-column variance from injection in capillary liquid chromatography. (United States)

    Aggarwal, Pankaj; Liu, Kun; Sharma, Sonika; Lawson, John S; Dennis Tolley, H; Lee, Milton L


    Efficiency and resolution in capillary liquid chromatography (LC) can be significantly affected by extra-column band broadening, especially for isocratic separations. This is particularly a concern in evaluating column bed structure using non-retained test compounds. The band broadening due to an injector supplied with a commercially available capillary LC system was characterized from experimental measurements. The extra-column variance from the injection valve was found to have an extra-column contribution independent of the injection volume, showing an exponential dependence on flow rate. The overall extra-column variance from the injection valve was found to vary from 34 to 23 nL. A new mathematical model was derived that explains this exponential contribution of extra-column variance on chromatographic performance. The chromatographic efficiency was compromised by ∼130% for a non-retained analyte because of injection valve dead volume. The measured chromatographic efficiency was greatly improved when a new nano-flow pumping system with integrated injection valve was used. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Open tubular capillary column for the separation of cytochrome C tryptic digest in capillary electrochromatography. (United States)

    Ali, Faiz; Cheong, Won Jo


    A silica capillary of 50 μm internal diameter and 500 mm length (416 mm effective length) was chemically modified with 4-(trifluoromethoxy) phenyl isocyanate in the presence of dibutyl tin dichloride as catalyst. Sodium diethyl dithiocarbamate was reacted with the terminal halogen of the bound ligand to incorporate the initiator moiety, and in situ polymerization was performed using a monomer mixture of styrene, N-phenylacrylamide, and methacrylic acid. The resultant open tubular capillary column immobilized with the copolymer layer was used for the separation of tryptic digest of cytochrome C in capillary electrochromatography. The sample was well eluted and separated into many components. The elution patterns of tryptic digest of cytochrome C were studied with respect to pH and water content in the mobile phase. This preliminary study demonstrates that open tubular capillary electrochromatography columns with a modified copolymer layer composed of proper nonpolar and polar units fabricated by reversible addition-fragmentation transfer polymerization can be useful as separation media for proteomic analysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Rice Husk Supported Catalysts for Degradation of Chlorobenzenes in Capillary Microreactor

    Directory of Open Access Journals (Sweden)

    Abdulelah Thabet


    Full Text Available Chlorinated organic pollutants are persistent, toxic, and ubiquitously distributed environmental contaminants. These compounds are highly bioaccumulative and adversely affect the ozone layer in the atmosphere. As such, their widespread usage is a major cause of environmental and health concern. Therefore, it is important to detoxify such compounds by environment friendly methods. In this work, rice husk supported platinum (RHA-Pt and titanium (RHA-Ti catalysts were used, for the first time, to investigate the detoxification of chlorobenzenes in a glass capillary microreactor. High potential (in kV range was applied to a reaction mixture containing buffer solution in the presence of catalyst. Due to high potential, hydroxyl and hydrogen radicals were produced, and the reaction was monitored by gas chromatography-mass spectrometry. The main advantage of this capillary reactor is the in situ generation of hydrogen for the detoxification of chlorobenzene. Various experimental conditions influencing detoxification were optimized. Reaction performance of capillary microreactor was compared with conventional catalysis. Only 20 min is sufficient to completely detoxify chlorobenzene in capillary microreactor compared to 24 h reaction time in conventional catalytic method. The capillary microreactor is simple, easy to use, and suitable for the detoxification of a wide range of chlorinated organic pollutants.

  5. Electrochemical properties of columns in capillary electrochromatography. I. Ohm's law, resistivity and field strength. (United States)

    Henry, Michael P; Ratnayake, Chitra K


    The most commonly used type of column in capillary electrochromatography (CEC) consists of a packed segment and an open (but buffer-filled) segment. The two segments differ importantly in two respects: firstly, their electrical resistivity; and secondly, their zeta potentials at a multitude of solid-liquid interfaces. Determination of the magnitude of these properties for each segment cannot be made using only results from the column as a whole. Instead, measurements of resistivity and zeta potentials of an entirely open, unpacked column can be used in conjunction with those of the CEC column to determine the electrochemical nature of both segments. This review of basic electrochemical properties will describe simple procedures that can be used to determine resistance, resistivity, conductivity, conductance, and field strength in each segment. In addition, it will be shown how the properties of each segment add together to give the same properties of the CEC column as a whole. The equations so derived will be applied to data from the literature and conclusions drawn from the results.

  6. Effective non-denaturing purification method for improving the solubility of recombinant actin-binding proteins produced by bacterial expression. (United States)

    Chung, Jeong Min; Lee, Sangmin; Jung, Hyun Suk


    Bacterial expression is commonly used to produce recombinant and truncated mutant eukaryotic proteins. However, heterologous protein expression may render synthesized proteins insoluble. The conventional method used to express a poorly soluble protein, which involves denaturation and refolding, is time-consuming and inefficient. There are several non-denaturing approaches that can increase the solubility of recombinant proteins that include using different bacterial cell strains, altering the time of induction, lowering the incubation temperature, and employing different detergents for purification. In this study, we compared several non-denaturing protocols to express and purify two insoluble 34 kDa actin-bundling protein mutants. The solubility of the mutant proteins was not affected by any of the approaches except for treatment with the detergent sarkosyl. These results indicate that sarkosyl can effectively improve the solubility of insoluble proteins during bacterial expression. Copyright © 2016. Published by Elsevier Inc.

  7. Denaturation and Oxidative Stability of Hemp Seed (Cannabis sativa L.) Protein Isolate as Affected by Heat Treatment. (United States)

    Raikos, Vassilios; Duthie, Garry; Ranawana, Viren


    The present study investigated the impact of heat treatments on the denaturation and oxidative stability of hemp seed protein during simulated gastrointestinal digestion (GID). Heat-denatured hemp protein isolate (HPI) solutions were prepared by heating HPI (2 mg/ml, pH 6.8) to 40, 60, 80 and 100 °C for 10 min. Heat-induced denaturation of the protein isolates was monitored by polyacrylamide gel electrophoresis. Heating HPI at temperatures above 80 °C significantly reduced solubility and led to the formation of large protein aggregates. The isolates were then subjected to in vitro GID and the oxidative stability of the generated peptides was investigated. Heating did not significantly affect the formation of oxidation products during GID. The results suggest that heat treatments should ideally remain below 80 °C if heat stability and solubility of HPI are to be preserved.

  8. From commodity polymers to functional polymers. (United States)

    Xiang, Tao; Wang, Ling-Ren; Ma, Lang; Han, Zhi-Yuan; Wang, Rui; Cheng, Chong; Xia, Yi; Qin, Hui; Zhao, Chang-Sheng


    Functional polymers bear specified chemical groups, and have specified physical, chemical, biological, pharmacological, or other uses. To adjust the properties while keeping material usage low, a method for direct synthesis of functional polymers is indispensable. Here we show that various functional polymers can be synthesized by in situ cross-linked polymerization/copolymerization. We demonstrate that the polymers synthesized by the facile method using different functional monomers own outstanding pH-sensitivity and pH-reversibility, antifouling property, antibacterial, and anticoagulant property. Our study opens a route for the functionalization of commodity polymers, which lead to important advances in polymeric materials applications.

  9. Monitoring and scoring counter-diffusion protein crystallization experiments in capillaries by in situ dynamic light scattering. (United States)

    Oberthuer, Dominik; Melero-García, Emilio; Dierks, Karsten; Meyer, Arne; Betzel, Christian; Garcia-Caballero, Alfonso; Gavira, Jose A


    In this paper, we demonstrate the feasibility of using in situ Dynamic Light Scattering (DLS) to monitor counter-diffusion crystallization experiments in capillaries. Firstly, we have validated the quality of the DLS signal in thin capillaries, which is comparable to that obtained in standard quartz cuvettes. Then, we have carried out DLS measurements of a counter-diffusion crystallization experiment of glucose isomerase in capillaries of different diameters (0.1, 0.2 and 0.3 mm) in order to follow the temporal evolution of protein supersaturation. Finally, we have compared DLS data with optical recordings of the progression of the crystallization front and with a simulation model of counter-diffusion in 1D.

  10. Monitoring and scoring counter-diffusion protein crystallization experiments in capillaries by in situ dynamic light scattering.

    Directory of Open Access Journals (Sweden)

    Dominik Oberthuer

    Full Text Available In this paper, we demonstrate the feasibility of using in situ Dynamic Light Scattering (DLS to monitor counter-diffusion crystallization experiments in capillaries. Firstly, we have validated the quality of the DLS signal in thin capillaries, which is comparable to that obtained in standard quartz cuvettes. Then, we have carried out DLS measurements of a counter-diffusion crystallization experiment of glucose isomerase in capillaries of different diameters (0.1, 0.2 and 0.3 mm in order to follow the temporal evolution of protein supersaturation. Finally, we have compared DLS data with optical recordings of the progression of the crystallization front and with a simulation model of counter-diffusion in 1D.

  11. Chemical denaturation of globular proteins at the air/water interface: an x-ray and neutron reflectometry study

    International Nuclear Information System (INIS)

    Perriman, A.W.; Henderson, M.J.; White, J.W.


    Full text: X-ray and neutron reflectometry has been used to probe the equilibrium surface structure of hen egg white lysozyme (lysozyme) and bovine β -lactoglobulin (β -lactoglobulin) under denaturing conditions at the air-water interface. This was achieved by performing experiments on 10 mg mL -1 protein solutions containing increasing concentrations of the chemical denaturant guanidinium hydrochloride (G.HCl). For solutions containing no G.HCl, the surface structure of the proteins was represented by a two-layer model with total thicknesses of 48 Angstroms and 38 Angstroms for lysozyme and β -lactoglobulin, respectively. The total volume of a single protein molecule and the associated water molecules was evaluated to be approximately 45 (0.3) nm 3 for lysozyme, and 60 (0.3) nm 3 for β-lactoglobulin. The thickness dimensions and the total volumes compared favourably with the crystal dimensions of 45 x 30 x 30 Angstroms (40.5 nm 3 ),1 and 36 x 36 x 36 Angstroms (47 nm 3 ) 2 for lysozyme and β -lactoglobulin, respectively. This comparison suggests that when no denaturant was present, the structures of lysozyme and β -lactoglobulin were near to their native conformations at the air-water interface. The response to the presence of the chemical denaturant was different for each protein. The surface layer of β-lactoglobulin expanded at very low concentrations (0.2 mol dm -3 ) of G.HCl. In contrast, the lysozyme layer contracted. At higher concentrations, unfolding of both the proteins led to the formation of a third diffuse layer. In general, lysozyme appeared to be less responsive to the chemical denaturant, which is most likely a result of the higher disulfide content of lysozyme. A protocol allowing quantitative thermodynamic analysis of the contribution from the air-water interface to the chemical denaturation of a protein was developed

  12. A calorimetric study of the interactions in the aqueous solutions of lysozyme in the presence of denaturing cosolvents

    International Nuclear Information System (INIS)

    Castronuovo, Giuseppina; Niccoli, Marcella


    Highlights: ► A thermodynamic method is reported to monitor the chemical denaturation of lysozyme. ► The enthalpic interaction coefficients are very useful parameters to gain information about the mechanism through which two hydrated molecules interact in solution. ► Hypotheses are proposed about the mechanism underlying the denaturation of lysozyme induced by high concentrations of urea or ethanol. - Abstract: A thermodynamic method is reported to monitor the chemical denaturation of lysozyme. Heats of dilution of the protein in concentrated aqueous solutions of urea or ethanol have been determined at 298.15 K by flow microcalorimetry. The pairwise enthalpic interaction coefficients of the protein in the different solvent media are derived. These parameters allow to gain information about the influence of the cosolvents on the interactions acting between two interacting hydrated molecules of lysozyme, hence on the denaturation process. At increasing urea concentration, up to about 6 mol kg −1 , the values of the interaction coefficients are large and negative and remain almost unaltered. The invariance of the coefficients underlines that, even in highly concentrated urea, the hydration shell of the protein is such to maintain essentially unaltered the native conformation. At higher urea concentrations, a sudden change in the sign of the coefficients monitors the variation in the interactions between two hydrated denatured protein molecules. The same trend is found when ethanol is the cosolvent. At increasing concentration of the cosolvent, coefficients are, at first, almost invariant. After that, denaturation occurs, detected as a jump toward much more negative values. The results obtained are rationalized on the basis of those previously found for small model molecules in concentrated solutions of urea or ethanol. The thermodynamic framework allows useful comments to be made on the possible mode of action of the two cosolvents on the stability of proteins

  13. Glutamate Induced Thermal Equilibrium Intermediate and Counteracting Effect on Chemical Denaturation of Proteins. (United States)

    Anumalla, Bramhini; Prabhu, N Prakash


    When organisms are subjected to stress conditions, one of their adaptive responses is accumulation of small organic molecules called osmolytes. These osmolytes affect the structure and stability of the biological macromolecules including proteins. The present study examines the effect of a negatively charged amino acid osmolyte, glutamate (Glu), on two model proteins, ribonuclease A (RNase A) and α-lactalbumin (α-LA), which have positive and negative surface charges at pH 7, respectively. These proteins follow two-state unfolding transitions during both heat and chemical induced denaturation processes. The addition of Glu stabilizes the proteins against temperature and induces an early equilibrium intermediate during unfolding. The stability is found to be enthalpy-driven, and the free energy of stabilization is more for α-LA compared to RNase A. The decrease in the partial molar volume and compressibility of both of the proteins in the presence of Glu suggests that the proteins attain a more compact state through surface hydration which could provide a more stable conformation. This is also supported by molecule dynamic simulation studies which demonstrate that the water density around the proteins is increased upon the addition of Glu. Further, the intermediates could be completely destabilized by lower concentrations (∼0.5 M) of guanidinium chloride and salt. However, urea subverts the Glu-induced intermediate formed by α-LA, whereas it only slightly destabilizes in the case of RNase A which has a positive surface charge and could possess charge-charge interactions with Glu. This suggests that, apart from hydration, columbic interactions might also contribute to the stability of the intermediate. Gdm-induced denaturation of RNase A and α-LA in the absence and the presence of Glu at different temperatures was carried out. These results also show the Glu-induced stabilization of both of the proteins; however, all of the unfolding transitions followed two

  14. Biological function evaluation and effects of laser micro-pore burn-denatured acellular dermal matrix. (United States)

    Zhang, Youlai; Zeng, Yuanlin; Xin, Guohua; Zou, Lijin; Ding, Yuewei; Duyin, Jiang


    In the field of burns repairs, many problems exist in the shortage of donor skin, the expense of allograft or xenograft skin, temporary substitution and unsatisfactory extremity function after wound healing. Previous studies showed that burn-denatured skin could return to normal dermis formation and function. This study investigates the application of laser micro-pore burn-denatured acellular dermis matrix (DADM) from an escharotomy in the repair of burn wounds and evaluates the biological properties and wound repair effects of DADM in implantation experiments in Kunming mice. Specific-pathogen-free (SPF) Kunming mice were used in this study. A deep II° burn wound was created on the dorsum of the mice by an electric heated water bath. The full-thickness wound tissue was harvested. The necrotic tissue and subcutaneous tissue were removed. The denatured dermis was preserved and treated with 0.25% trypsin, 0.5% Triton X-100. The DADM was drilled by laser micro-pore. The biological properties and grafting effects of laser micro-pore burn-DADM were evaluated by morphology, cytokine expression levels and subcutaneous implantation experiments in Kunming mice. We found statistical significance (Ppore burn-DADM (experimental group) compared to the control group (no laser micro-pore burn-DADM). Cytokine expression level was different in the dermal matrixes harvested at various time points after burn (24h, 48h, 72h and infected wound group). Comparing the dermal matrix from 24h burn tissue to infected wound tissue, the expression level of IL-6, MMP-24, VE-cadherin and VEGF were decreased. We found no inflammatory cells infiltration in the dermal matrix were observed in both experimental and control groups (24h burn group), while the obviously vascular infiltration and fiber fusion were observed in the experimental group after subcutaneous implantation experiments. There was better bio-performance, low immunogenicity and better dermal incorporation after treated by laser

  15. Hyperthermophile protein behavior: partially-structured conformations of Pyrococcus furiosus rubredoxin monomers generated through forced cold-denaturation and refolding.

    Directory of Open Access Journals (Sweden)

    Sanjeev Kumar Chandrayan

    Full Text Available Some years ago, we showed that thermo-chemically denatured, partially-unfolded forms of Pyrococcus furiosus triosephosphateisomerase (PfuTIM display cold-denaturation upon cooling, and heat-renaturation upon reheating, in proportion with the extent of initial partial unfolding achieved. This was the first time that cold-denaturation was demonstrated for a hyperthermophile protein, following unlocking of surface salt bridges. Here, we describe the behavior of another hyperthermophile protein, the small, monomeric, 53 residues-long rubredoxin from Pyrococcus furiosus (PfRd, which is one of the most thermostable proteins known to man. Like PfuTIM, PfRd too displays cold-denaturation after initial thermo-chemical perturbation, however, with two differences: (i PfRd requires considerably higher temperatures as well as higher concentrations of guanidium hydrochloride (Gdm.HCl than PfuTIM; (ii PfRd's cold-denaturation behavior during cooling after thermo-chemical perturbation is incompletely reversible, unlike PfuTIM's, which was clearly reversible (from each different conformation generated. Differential cold-denaturation treatments allow PfRd to access multiple partially-unfolded states, each of which is clearly highly kinetically-stable. We refer to these as 'Trishanku' unfolding intermediates (or TUIs. Fascinatingly, refolding of TUIs through removal of Gdm.HCl generates multiple partially-refolded, monomeric, kinetically-trapped, non-native 'Trishanku' refolding intermediates (or TRIs, which differ from each other and from native PfRd and TUIs, in structural content and susceptibility to proteolysis. We find that the occurrence of cold denaturation and observations of TUI and TRI states is contingent on the oxidation status of iron, with redox agents managing to modulate the molecule's behavior upon gaining access to PfRd's iron atom. Mass spectrometric examination provides no evidence of the formation of disulfide bonds, but other experiments

  16. Structure and properties of native and unfolded lysing enzyme from T. harzianum: Chemical and pH denaturation. (United States)

    Bey, Houda; Gtari, Wala; Aschi, Adel; Othman, Tahar


    The effect of chemical denaturants and pH on the change of the conformation of the protein Lysing Enzyme from Trichoderma Harzianum has been investigated by dynamic light scattering (DLS) and turbidimetry. Chemical denaturants are frequently used to describe the mechanisms of folding and transition states. We have analyzed the pH effect on the properties and particle size of the protein. The compaction factor CI has shown that the protein is weakly disordered. The molecular dynamics simulations confirm, at neutral pH, that the protein has a low net charge and high hydrophobicity. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Mercury(II) binds to both of chymotrypsin's histidines, causing inhibition followed by irreversible denaturation/aggregation


    Stratton, Amanda; Ericksen, Matthew; Harris, Travis V.; Symmonds, Nick; Silverstein, Todd P.


    The toxicity of mercury is often attributed to its tight binding to cysteine thiolate anions in vital enzymes. To test our hypothesis that Hg(II) binding to histidine could be a significant factor in mercury's toxic effects, we studied the enzyme chymotrypsin, which lacks free cysteine thiols; we found that chymotrypsin is not only inhibited, but also denatured by Hg(II). We followed the aggregation of denatured enzyme by the increase in visible absorbance due to light scattering. Hg(II)‐indu...

  18. Shape memory polymers (United States)

    Wilson, Thomas S.; Bearinger, Jane P.


    New shape memory polymer compositions, methods for synthesizing new shape memory polymers, and apparatus comprising an actuator and a shape memory polymer wherein the shape memory polymer comprises at least a portion of the actuator. A shape memory polymer comprising a polymer composition which physically forms a network structure wherein the polymer composition has shape-memory behavior and can be formed into a permanent primary shape, re-formed into a stable secondary shape, and controllably actuated to recover the permanent primary shape. Polymers have optimal aliphatic network structures due to minimization of dangling chains by using monomers that are symmetrical and that have matching amine and hydroxyl groups providing polymers and polymer foams with clarity, tight (narrow temperature range) single transitions, and high shape recovery and recovery force that are especially useful for implanting in the human body.

  19. Microstructural, protein denaturation and water holding properties of lamb under pulse vacuum brining. (United States)

    Wang, Zhenyu; Xu, Weiwei; Kang, Ning; Shen, Qingwu; Zhang, Dequan


    The objective of this study was to investigate the microstructure, protein denaturation and water holding capacity of lamb pickled under pulse vacuum. Sixty topside samples (M. semimembranosus) were randomly assigned into two groups and cured for 0, 1.5, 3, 4.5 and 6h by pulse vacuum brining (PVB) and atmospheric brining (AB) (control), respectively. The salt content of samples by PVB was about 1% higher than AB from 1.5h to 6h. The water holding capacity was greater for PVB group before 4.5h (Pvacuum brining can be used to improve the brining efficiency, promoting the actomyosin dissociation and improving the water holding capacity of lamb, which will be a potential technology to be used in practice. Copyright © 2015. Published by Elsevier Ltd.

  20. Investigating the fermentation of cocoa by correlating denaturing gradient gel electrophoresis profiles and near infrared spectra

    DEFF Research Database (Denmark)

    Nielsen, Dennis Sandris; Snitkjær, Pia; van der Berg, Franciscus Winfried J


    Raw cocoa has an astringent, unpleasant taste and flavour, and has to be fermented, dried and roasted in order to obtain the characteristic cocoa flavour and taste. During the fermentation microbial activity outside the cocoa beans induces biochemical and physical changes inside the beans...... of the beans and the chemical processes inside the beans have been carried out previously. Recently it has been shown that Denaturing Gradient Gel Electrophoresis (DGGE) offers an efficient tool for monitoring the microbiological changes taking place during the fermentation of cocoa. Near Infrared (NIR......) spectroscopy has previously been used to determine various components in cocoa beans, offering a rapid alternative compared to traditional analytical methods for obtaining knowledge about changes in the chemical composition of the cocoa beans during fermentation. During a number of cocoa fermentations bean...

  1. 125I-labeled cortisol radioimmunoassay in which serum binding protein are enzymatically denatured

    International Nuclear Information System (INIS)

    Hasler, M.J.; Painter, K.; Niswender, G.D.


    We report an iodine-125 radioimmunoassay for cortisol in biological fluids, in which interfering binding proteins are enzymatically denatured. An antiserum to cortisol-3-carboxymethyloxime-bovine serum albumin, extremely low cross-reacting with other corticosteroids, was raised in rabbits. A cortisol-3-carboxymethyloxime tyrosine methyl ester derivative was synthesized and labeled with iodine-125 by standard radioiodination techniques. To eliminate the need for extraction and recovery procedures, we digested interfering binding with a proteolytic enzyme, which then was heat-inactivated before adding the labeled derivative and the premixed, preincubated antiserum complex. There was quantitative analytical recovery of esogenous cortisol added to sera from a normal man, a normal woman, and a pregnant woman. Values for the same samples agreed after extraction and chromatographic purification and agreed well with values obtained by other techniques by independent reference laboratories. The five-step assay can be done in 6 h or less

  2. Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II. (United States)

    Nemtseva, Elena V; Lashchuk, Olesya O; Gerasimova, Marina A; Melnik, Tatiana N; Nagibina, Galina S; Melnik, Bogdan S


    In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

  3. Motion of liquid plugs between vapor bubbles in capillary tubes: a comparison between fluids (United States)

    Bertossi, Rémi; Ayel, Vincent; Mehta, Balkrishna; Romestant, Cyril; Bertin, Yves; Khandekar, Sameer


    Pulsating heat pipes (PHP) are now well-known devices in which liquid/vapor slug flow oscillates in a capillary tube wound between hot and cold sources. In this context, this paper focuses on the motion of the liquid plug, trapped between vapor bubbles, moving in capillary tubes, to try to better understand the thermo-physical phenomena involved in such devices. This study is divided into three parts. In the first part, an experimental study presents the evolution of the vapor pressure during the evaporation process of a liquid thin film deposited from a liquid plug flowing in a heated capillary tube: it is found that the behavior of the generated and removed vapor can be very different, according to the thermophysical properties of the fluids. In the second part, a transient model allows to compare, in terms of pressure and duration, the motion of a constant-length liquid plug trapped between two bubbles subjected to a constant difference of vapor pressure: the results highlight that the performances of the four fluids are also very different. Finally, a third model that can be considered as an improvement of the second one, is also presented: here, the liquid slug is surrounded by two vapor bubbles, one subjected to evaporation, the pressure in both bubbles is now a result of the calculation. This model still allows comparing the behaviors of the fluid. Even if our models are quite far from a complete model of a real PHP, results do indicate towards the applicability of different fluids as suitable working fluids for PHPs, particularly in terms of the flow instabilities which they generate.

  4. Multi-scale simulation of asphaltene aggregation and deposition in capillary flow. (United States)

    Boek, Edo S; Headen, Thomas F; Padding, Johan T


    Asphaltenes are known as the 'cholesterol' of crude oil. They form nano-aggregates, precipitate, adhere to surfaces, block rock pores and may alter the wetting characteristics of mineral surfaces within the reservoir, hindering oil recovery efficiency. Despite a significant research effort, the structure, aggregation and deposition of asphaltenes under flowing conditions remain poorly understood. For this reason, we have investigated asphaltenes, their aggregation and their deposition in capillary flow using multi-scale simulations and experiments. At the colloid scale, we use a hybrid simulation approach: for the solvent, we used the stochastic rotation dynamics (also known as multi particle collision dynamics) simulation method, which provides both hydrodynamics and Brownian motion. This is coupled to a coarse-grained MD approach for the asphaltene colloids. The colloids interact through a screened Coulomb potential with varying well depth epsilon. We tune the flow rate to obtain Pe(flow) > 1 (hydrodynamic interactions dominate) and Re force (PMF) between pairs of asphaltene molecules in an explicit solvent. We obtain a reasonable fit using a -1/r2 attraction for the attractive tail of the PMF at intermediate distances. We speculate that this is due to the two-dimensional nature of the asphaltene molecules. Finally, we discuss how we can relate this interaction to the mesoscopic colloid aggregate interaction. We assume that the colloidal aggregates consist of nano-aggregates. Taking into account observed solvent entrainment effects, we deduct the presence of lubrication layers between the nano-aggregates, which leads to a significant screening of the direct asphaltene-asphaltene interactions.

  5. Microbial Community Structure of Korean Cabbage Kimchi and Ingredients with Denaturing Gradient Gel Electrophoresis. (United States)

    Hong, Sung Wook; Choi, Yun-Jeong; Lee, Hae-Won; Yang, Ji-Hee; Lee, Mi-Ai


    Kimchi is a traditional Korean fermented vegetable food, the production of which involves brining of Korean cabbage, blending with various other ingredients (red pepper powder, garlic, ginger, salt-pickled seafood, etc.), and fermentation. Recently, kimchi has also become popular in the Western world because of its unique taste and beneficial properties such as antioxidant and antimutagenic activities, which are derived from the various raw materials and secondary metabolites of the fermentative microorganisms used during production. Despite these useful activities, analysis of the microbial community present in kimchi has received relatively little attention. The objective of this study was to evaluate the bacterial community structure from the raw materials, additives, and final kimchi product using the culture-independent method. Specifically, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the 16S rRNA partial sequences of the microflora. One primer set for bacteria, 341F(GC)-518R, reliably produced amplicons from kimchi and its raw materials, and these bands were clearly separated on a 35-65% denaturing gradient gel. Overall, 117 16S rRNA fragments were identified by PCR-DGGE analysis. Pediococcus pentosaceus, Leuconostoc citreum, Leuconostoc gelidum, and Leuconostoc mesenteroides were the dominant bacteria in kimchi. The other strains identified were Tetragenococcus, Pseudomonas, Weissella, and uncultured bacterium. Comprehensive analysis of these microorganisms could provide a more detailed understanding of the biologically active components of kimchi and help improve its quality. PCR-DGGE analysis can be successfully applied to a fermented food to detect unculturable or other species.

  6. Aqueous Solutions of the Ionic Liquid 1-butyl-3-methylimidazolium Chloride Denature Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Baker, Gary A [ORNL; Heller, William T [ORNL


    As we advance our understanding, ionic liquids (ILs) are finding ever broader scope within the chemical sciences including, most recently, pharmaceutical, enzymatic, and bioanalytical applications. With examples of enzymatic activity reported in both neat ILs and in IL/water mixtures, enzymes are frequently assumed to adopt a quasi-native conformation, even if little work has been carried out to date toward characterizing the conformation, dynamics, active-site perturbation, cooperativity of unfolding transitions, free energy of stabilization, or aggregation/oligomerization state of enzymes in the presence of an IL solvent component. In this study, human serum albumin and equine heart cytochrome c were characterized in aqueous solutions of the fully water-miscible IL 1-butyl-3-methylimidazolium chloride, [bmim]Cl, by small-angle neutron and X-ray scattering. At [bmim]Cl concentrations up to 25 vol.%, these two proteins were found to largely retain their higher-order structures whereas both proteins become highly denatured at the highest IL concentration studied here (i.e., 50 vol.% [bmim]Cl). The response of these proteins to [bmim]Cl is analogous to their behavior in the widely studied denaturants guanidine hydrochloride and urea which similarly lead to random coil conformations at excessive molar concentrations. Interestingly, human serum albumin dimerizes in response to [bmim]Cl, whereas cytochrome c remains predominantly in monomeric form. These results have important implications for enzymatic studies in aqueous IL media, as they suggest a facile pathway through which biocatalytic activity can be altered in these nascent and potentially green electrolyte systems.

  7. Role of conductivity for the production of charge patches by ions guided in capillaries (United States)

    Stolterfoht, N.; Herczku, P.; Juhász, Z.; Kovács, S. T. S.; Rácz, R.; Biri, S.; Sulik, B.


    Guiding of 3-keV Ne7+ ion through nanocapillaries in highly insulating polymers was studied. By means of simulations it is made evident that oscillations of the ion emission angle after transmission through capillaries reveals charge patches within the capillaries. The creation and removal of the charge patches depend on the conductivity of the capillaries so that a relationship of the conductivity and the oscillatory structure of the mean ion emission angle can be established. Experimentally significant differences were found in the ion fractions transmitted through capillaries prepared in polycarbonate (PC) and polyethylene terephthalate (PET). For PC the ion fraction decreases with inserted charge indicating blocking effects on the transmitted ions whereas for PET the ion transmission was found to be almost constant even for long term irradiation. The observed differences were attributed to different conductivities of the capillaries in the polymer materials. This attribution was supported by additional measurements concerning the oscillatory structures of the ion emission angles.

  8. Polymer nanocomposites: polymer and particle dynamics

    KAUST Repository

    Kim, Daniel


    Polymer nanocomposites containing nanoparticles smaller than the random coil size of their host polymer chains are known to exhibit unique properties, such as lower viscosity and glass transition temperature relative to the neat polymer melt. It has been hypothesized that these unusual properties result from fast diffusion of the nanostructures in the host polymer, which facilitates polymer chain relaxation by constraint release and other processes. In this study, the effects of addition of sterically stabilized inorganic nanoparticles to entangled cis-1,4-polyisoprene and polydimethylsiloxane on the overall rheology of nanocomposites are discussed. In addition, insights about the relaxation of the host polymer chains and transport properties of nanoparticles in entangled polymer nanocomposites are presented. The nanoparticles are found to act as effective plasticizers for their entangled linear hosts, and below a critical, chemistry and molecular-weight dependent particle volume fraction, lead to reduced viscosity, glass transition temperature, number of entanglements, and polymer relaxation time. We also find that the particle motions in the polymer host are hyperdiffusive and at the nanoparticle length scale, the polymer host acts like a simple, ideal fluid and the composites\\' viscosity rises with increasing particle concentration. © 2012 The Royal Society of Chemistry.

  9. Small angle X-ray studies of protein-polymer interactions

    International Nuclear Information System (INIS)

    Torriani, Iris; Oliveira, Cristiano L.P. de; Almeida, Nara L.; Loh, Watson


    Full text: The interaction between biological macromolecules and non-adsorbing polymers is considered of utmost importance in the study of protein crystallization processes and in the study of a large number of protein-polymer systems or artificial surfaces used in medical procedures, in which polymeric materials are in contact with blood proteins. The structural information furnished by small angle X-ray scattering (SAXS) experiments can be used to describe protein-polymer interaction in solution mixtures considering the dispersion as a two-component system. In this work, two proteins, lysozyme and bovine serum albumin (BSA), were studied in the presence of Poly(ethylene oxide) (PEO), various EO/PO copolymers of varied composition and Poly(ethylene glycol) (PEG). Thermal stability of both lysozyme and BSA was studied in the presence of these polymers. X-ray scattering experiments were performed at the SAXS beamline of the Laboratorio Nacional de Luz Sincrotron, Campinas, SP, using the facility available for liquid dispersions under controlled temperature. Room temperature measurements were aimed at detecting possible polymer-protein interactions. Thermal denaturation processes were studied in some of these systems in order to check the stabilizing effect of some of the polymers used, at fixed temperatures of 25, 50, 60 and 70 deg C. At 80 deg C, using a real time data acquisition system, structural changes could be followed as a function of time in a sequence of frames that show denaturation and aggregation of the proteins. Real space analysis of the intensity functions was performed using a mathematical expression derived for the form factor of a system of particles of different shapes. The pair distance distribution functions of each component of the system could be calculated separately. The possibility of complex formation in the case of the proteins studied is not supported by our results. The presence of polymers may affect the protein-protein interaction

  10. Polymerase chain reaction and denaturing gradient gel electrophoresis monitoring of fecal Bifidobacterium populations in a prebiotic and probiotic feeding trial

    NARCIS (Netherlands)

    Satokari, R.M.; Vaughan, E.E.; Akkermans, A.D.L.; Vos, de W.M.


    A culture-independent approach based on genus-specific PCR and denaturing gradient gel electrophoresis (DGGE) was used to monitor qualitative changes in fecal bifidobacterial communities in a human feeding trial. DNA was extracted directly from feces and bifidobacterial 16S rDNA sequences were

  11. Reaction of Native and Denatured Brucella abortus (S19 Proteins with Antibody Using Affinity Chromatography and Immunoblotting

    Directory of Open Access Journals (Sweden)

    R. Karimi


    Full Text Available Western blotting or immunoblotting commonly use for study of reaction between antigens and antibodies. Denaturation of many proteins in immunoblotting can affect greatly the reactivity of antibodies and outcome of the procedure.In this study proteins of Brucella abortus (S19 was extracted by a mild method and reaction of the extracted proteins with serum of infected human and goat and immunized rabbit compared by affinity chromatography and immunoblotting. Gamma globulin (mostly IgG fraction of the sera was precipitated by half saturation of ammonium sulfate and linked to activated sepharose 4B. The extracted proteins were loaded on the affinity column. Attached proteins was eluted by low pH and analyzed by SDS-PAGE. Reaction of the total extract and eluted fractions with IgG fraction of sera was evaluated by Western blotting.Upon the results of affinity chromatography and immunoblotting, Brucella proteins can be classified in four groups: 1- The proteins that adsorbed to the affinity column and react with IgG in westernblotting. 2- Proteins that react with IgG in native state but no in denatured state. 3- Proteins that do not react with IgG in native state but react in denatured state. 4- Proteins that do not react with IgG in native and denatured state.

  12. Evaluation of several techniques to modify denatured muscle tissue to obtain a scaffold for peripheral nerve regeneration

    NARCIS (Netherlands)

    Meek, MF; den Dunnen, WFA; Schakenraad, JM; Robinson, PH

    The aim of this study was to (1) evaluate the effect of several preparation techniques of denatured muscle tissue to obtain an open three-dimensional structure, and (2) test if this scaffold is suitable for peripheral nerve regeneration. Four samples (A-D) of muscle tissue specimens were evaluated

  13. High-intensity focused ultrasound monitoring using harmonic motion imaging for focused ultrasound (HMIFU) under boiling or slow denaturation conditions. (United States)

    Hou, Gary Y; Marquet, Fabrice; Wang, Shutao; Apostolakis, Iason-Zacharias; Konofagou, Elisa E


    Harmonic motion imaging for focused ultrasound (HMIFU) is a recently developed high-intensity focused ultrasound (HIFU) treatment monitoring method that utilizes an amplitude-modulated therapeutic ultrasound beam to induce an oscillatory radiation force at the HIFU focus and estimates the focal tissue displacement to monitor the HIFU thermal treatment. In this study, the performance of HMIFU under acoustic, thermal, and mechanical effects was investigated. The performance of HMIFU was assessed in ex vivo canine liver specimens (n = 13) under slow denaturation or boiling regimes. A passive cavitation detector (PCD) was used to assess the acoustic cavitation activity, and a bare-wire thermocouple was used to monitor the focal temperature change. During lesioning with slow denaturation, high quality displacements (correlation coefficient above 0.97) were observed under minimum cavitation noise, indicating the tissue initial-softening-then- stiffening property change. During HIFU with boiling, HMIFU monitored a consistent change in lesion-to-background displacement contrast (0.46 ± 0.37) despite the presence of strong cavitation noise due to boiling during lesion formation. Therefore, HMIFU effectively monitored softening-then-stiffening during lesioning under slow denaturation, and detected lesioning under boiling with a distinct change in displacement contrast under boiling in the presence of cavitation. In conclusion, HMIFU was shown under both boiling and slow denaturation regimes to be effective in HIFU monitoring and lesioning identification without being significantly affected by cavitation noise.

  14. Sequential Events in the Irreversible Thermal Denaturation of Human Brain-Type Creatine Kinase by Spectroscopic Methods

    Directory of Open Access Journals (Sweden)

    Yan-Song Gao


    Full Text Available The non-cooperative or sequential events which occur during protein thermal denaturation are closely correlated with protein folding, stability, and physiological functions. In this research, the sequential events of human brain-type creatine kinase (hBBCK thermal denaturation were studied by differential scanning calorimetry (DSC, CD, and intrinsic fluorescence spectroscopy. DSC experiments revealed that the thermal denaturation of hBBCK was calorimetrically irreversible. The existence of several endothermic peaks suggested that the denaturation involved stepwise conformational changes, which were further verified by the discrepancy in the transition curves obtained from various spectroscopic probes. During heating, the disruption of the active site structure occurred prior to the secondary and tertiary structural changes. The thermal unfolding and aggregation of hBBCK was found to occur through sequential events. This is quite different from that of muscle-type CK (MMCK. The results herein suggest that BBCK and MMCK undergo quite dissimilar thermal unfolding pathways, although they are highly conserved in the primary and tertiary structures. A minor difference in structure might endow the isoenzymes dissimilar local stabilities in structure, which further contribute to isoenzyme-specific thermal stabilities.

  15. Laboratory Exercise for Studying the Morphology of Heat-Denatured and Amyloid Aggregates of Lysozyme by Atomic Force Microscopy (United States)

    Gokalp, Sumeyra; Horton, William; Jónsdóttir-Lewis, Elfa B.; Foster, Michelle; Török, Marianna


    To facilitate learning advanced instrumental techniques, essential tools for visualizing biomaterials, a simple and versatile laboratory exercise demonstrating the use of Atomic Force Microscopy (AFM) in biomedical applications was developed. In this experiment, the morphology of heat-denatured and amyloid-type aggregates formed from a low-cost…

  16. Denaturation and in Vitro Gastric Digestion of Heat-Treated Quinoa Protein Isolates Obtained at Various Extraction pH

    NARCIS (Netherlands)

    Ruiz, Geraldine Avila; Opazo-Navarrete, Mauricio; Meurs, Marlon; Minor, Marcel; Sala, Guido; Boekel, van Tiny; Stieger, Markus; Janssen, Anja E.M.


    The aim of this study was to determine the influence of heat processing on denaturation and digestibility properties of protein isolates obtained from sweet quinoa (Chenopodium quinoa Willd) at various extraction pH values (8, 9, 10 and 11). Pretreatment of suspensions of protein isolates at 60,

  17. The effect of Na+ and K+ on the thermal denaturation of Na+ and + K+-dependent ATPase. (United States)

    Fischer, T H


    To increase our understanding of the physical nature of the Na+ and K+ forms of the Na+ + K+-dependent ATPase, thermal-denaturation studies were conducted in different types of ionic media. Thermal-denaturation measurements were performed by measuring the regeneration of ATPase activity after slow pulse exposure to elevated temperatures. Two types of experiments were performed. First, the dependence of the thermal-denaturation rate on Na+ and K+ concentrations was examined. It was found that both cations stabilized the pump protein. Also, K+ was a more effective stabilizer of the native state than was Na+. Secondly, a set of thermodynamic parameters was obtained by measuring the temperature-dependence of the thermal-denaturation rate under three ionic conditions: 60 mM-K+, 150 mM-Na+ and no Na+ or K+. It was found that ion-mediated stabilization of the pump protein was accompanied by substantial increases in activation enthalpy and entropy, the net effect being a less-pronounced increase in activation free energy. PMID:6309139

  18. Using a second-order differential model to fit data without baselines in protein isothermal chemical denaturation. (United States)

    Tang, Chuanning; Lew, Scott; He, Dacheng


    In vitro protein stability studies are commonly conducted via thermal or chemical denaturation/renaturation of protein. Conventional data analyses on the protein unfolding/(re)folding require well-defined pre- and post-transition baselines to evaluate Gibbs free-energy change associated with the protein unfolding/(re)folding. This evaluation becomes problematic when there is insufficient data for determining the pre- or post-transition baselines. In this study, fitting on such partial data obtained in protein chemical denaturation is established by introducing second-order differential (SOD) analysis to overcome the limitations that the conventional fitting method has. By reducing numbers of the baseline-related fitting parameters, the SOD analysis can successfully fit incomplete chemical denaturation data sets with high agreement to the conventional evaluation on the equivalent completed data, where the conventional fitting fails in analyzing them. This SOD fitting for the abbreviated isothermal chemical denaturation further fulfills data analysis methods on the insufficient data sets conducted in the two prevalent protein stability studies. © 2016 The Protein Society.

  19. New comprehensive denaturing-gradient-gel-electrophoresis assay for KRAS mutation detection applied to paraffin-embedded tumours

    NARCIS (Netherlands)

    Hayes, VM; Westra, JL; Verlind, E; Bleeker, W; Plukker, JT; Hofstra, RMW; Buys, CHCM


    A comprehensive mutation detection assay is presented for the entire coding region and all splice site junctions of the KRAS oncogene. The assay is based on denaturing gradient gel electrophoresis and applicable to archival paraffin-embedded tumour material. All KRAS amplicons are analysed within

  20. Polymers and radiation

    International Nuclear Information System (INIS)

    Zagorski, Z.


    The article is the broad review of history and state of art in radiation chemistry of polymers. The scientific background of radiation interaction with polymers and mechanisms of radiolytic degradation for aqueous solutions and 'dry' state of polymers have been shown. Also the applications of radiation for polymer properties modifications has been discussed in terms of polymers grafting and cross-linking for achieve shape memory feature, preparation of radioresistant polymers used for medical supplies being devoted to radiation sterilization etc. The polish contribution in related studies has been presented as well

  1. Conducting polymer materials

    Directory of Open Access Journals (Sweden)

    Jovanović Slobodan M.


    Full Text Available Conducting polymers represent a very interesting group of polymer materials Investigation of the synthesis, structure and properties of these materials has been the subject of considerable research efforts in the last twenty years. A short presentating of newer results obtained by investigating of the synthesis, structure and properties of two basic groups of conducting polymers: a conducting polymers the conductivity of which is the result of their molecular structure, and b conducting polymer composites (EPC, is given in this paper. The applications and future development of this group of polymer materials is also discussed.

  2. Hydrophobic clustering in nonnative states of a protein: Interpretation of chemical shifts in NMR spectra of denatured states of lysozyme

    International Nuclear Information System (INIS)

    Evans, P.A.; Topping, K.D.; Woolfson, D.N.; Dobson, C.M.


    Chemical shifts of resonances of specific protons in the 1H NMR spectrum of thermally denatured hen lysozyme have been determined by exchange correlation with assigned native state resonances in 2D NOESY spectra obtained under conditions where the two states are interconverting. There are subtle but widespread deviations of the measured shifts from the values which would be anticipated for a random coil; in the case of side chain protons these are virtually all net upfield shifts and it is shown that this may be the averaged effect of interactions with aromatic rings in a partially collapsed denatured state. In a very few cases, notably that of two sequential tryptophan residues, it is possible to interpret these effects in terms of specific, local interresidue interactions. Generally, however, there is no correlation with either native state shift perturbations or with sequence proximity to aromatic groups. Diminution of most of the residual shift perturbations on reduction of the disulfide cross-links confirms that they are not simply effects of residues adjacent in the sequence. Similar effects of chemical denaturants, with the disulfides intact, demonstrate that the shift perturbations reflect an enhanced tendency to side chain clustering in the thermally denatured state. The temperature dependences of the shift perturbations suggest that this clustering is noncooperative and is driven by small, favorable enthalpy changes. While the extent of conformational averaging is clearly much greater than that observed for a homologous protein, alpha-lactalbumin, in its partially folded molten globule state, the results clearly show that thermally denatured lysozyme differs substantially from a random coil, principally in that it is partially hydrophobically collapsed

  3. Scalable Patterning of MoS2Nanoribbons by Micromolding in Capillaries

    KAUST Repository

    Hung, Yu-Han


    In this study, we report a facile approach to prepare dense arrays of MoS2 nanoribbons by combining procedures of micromolding in capillaries (MIMIC) and thermolysis of thiosalts ((NH4)2MoS4) as the printing ink. The obtained MoS2 nanoribbons had a thickness reaching as low as 3.9 nm, a width ranging from 157 to 465 nm, and a length up to 2 cm. MoS2 nanoribbons with an extremely high aspect ratio (length/width) of ∼7.4 × 108 were achieved. The MoS2 pattern can be printed on versatile substrates, such as SiO2/Si, sapphire, Au film, FTO/glass, and graphene-coated glass. The degree of crystallinity of the as-prepared MoS2 was discovered to be adjustable by varying the temperature through postannealing. The high-temperature thermolysis (1000 °C) results in high-quality conductive samples, and field-effect transistors based on the patterned MoS2 nanoribbons were demonstrated and characterized, where the carrier mobility was comparable to that of thin-film MoS2. In contrast, the low-temperature-treated samples (170 °C) result in a unique nanocrystalline MoSx structure (x ≈ 2.5), where the abundant and exposed edge sites were obtained from highly dense arrays of nanoribbon structures by this MIMIC patterning method. The patterned MoSx was revealed to have superior electrocatalytic efficiency (an overpotential of ∼211 mV at 10 mA/cm2 and a Tafel slope of 43 mV/dec) in the hydrogen evolution reaction (HER) when compared to the thin-film MoS2. The report introduces a new concept for rapidly fabricating cost-effective and high-density MoS2/MoSx nanostructures on versatile substrates, which may pave the way for potential applications in nanoelectronics/optoelectronics and frontier energy materials. © 2016 American Chemical Society.

  4. Peak capacity and peak capacity per unit time in capillary and microchip zone electrophoresis. (United States)

    Foley, Joe P; Blackney, Donna M; Ennis, Erin J


    The origins of the peak capacity concept are described and the important contributions to the development of that concept in chromatography and electrophoresis are reviewed. Whereas numerous quantitative expressions have been reported for one- and two-dimensional separations, most are focused on chromatographic separations and few, if any, quantitative unbiased expressions have been developed for capillary or microchip zone electrophoresis. Making the common assumption that longitudinal diffusion is the predominant source of zone broadening in capillary electrophoresis, analytical expressions for the peak capacity are derived, first in terms of migration time, diffusion coefficient, migration distance, and desired resolution, and then in terms of the remaining underlying fundamental parameters (electric field, electroosmotic and electrophoretic mobilities) that determine the migration time. The latter expressions clearly illustrate the direct square root dependence of peak capacity on electric field and migration distance and the inverse square root dependence on solute diffusion coefficient. Conditions that result in a high peak capacity will result in a low peak capacity per unit time and vice-versa. For a given symmetrical range of relative electrophoretic mobilities for co- and counter-electroosmotic species (cations and anions), the peak capacity increases with the square root of the electric field even as the temporal window narrows considerably, resulting in a significant reduction in analysis time. Over a broad relative electrophoretic mobility interval [-0.9, 0.9], an approximately two-fold greater amount of peak capacity can be generated for counter-electroosmotic species although it takes about five-fold longer to do so, consistent with the well-known bias in migration time and resolving power for co- and counter-electroosmotic species. The optimum lower bound of the relative electrophoretic mobility interval [μ r,Z , μ r,A ] that provides the maximum

  5. Influence of solvent on temperature and thermal peak broadening in capillary zone electrophoresis. (United States)

    Porras, Simo P; Marziali, Ettore; Gas, Bohuslav; Kenndler, Ernst


    The present paper deals with the role of the solvent on thermal peak broadening. One main solvent property that determines the magnitude of the temperature gradient due to the generation of Joule heat in capillary zone electrophoresis is the thermal conductivity. As organic solvents have lower thermal conductivity than water (methanol and acetonitrile, e.g., nearly by a factor of 3) it can be hypothesized that the temperature gradient inside the capillary is more pronounced in organic solvents compared to an aqueous solution. On the other hand, the temperature dependence of the ion mobility (which is responsible for the velocity profile and thus for thermal peak broadening) is smaller in organic solvents. To get insight into the thermal effect of the solvent, first the temperature of a solution in a cylindrical tube was calculated utilizing the heat balance equation. It was shown that the two theoretical models most common in the literature (based on the analytical solution or on an assumption of the parabolic temperature profile in the tube, respectively) give the same results. The latter model was chosen for the further calculations, adding a quadratic term to express the electric conductivity as a function of the temperature. The temperature at the inner capillary wall and center as function of the capillary dimensions and the electric power was computed for electrolytes with a given conductivity at 25.0 degrees C with water, methanol, and acetonitrile as solvents. Capillary cooling systems used were circulating liquid cooling, enforced air-cooling, and natural convection in still air. The mean temperature (averaged over the cross section) resulting from Joule heating was compared with experimentally determined temperatures established upon application of an electric field; the latter temperature was derived from the measurement of the electric conductance of the background electrolyte solution and its (measured) temperature dependence. All investigations were

  6. Introduction to Polymer Chemistry. (United States)

    Harris, Frank W.


    Reviews the physical and chemical properties of polymers and the two major methods of polymer synthesis: addition (chain, chain-growth, or chain-reaction), and condensation (step-growth or step-reaction) polymerization. (JN)

  7. Antiviral Polymer Therapeutics

    DEFF Research Database (Denmark)

    Smith, Anton Allen Abbotsford


    polymerized in a controlled manner with carrier monomers of historically proven biocompatible polymers. The carrier polymers, the loading of ribavirin as well as the size of the polymer were varied systematically with the aid of an automated synthesis platform. These polymers were tested in a cellular assay...... of reversible-addition-fragmentation chain transfer polymerization, which not only controls the size of polymer, but also allows the introduction of a terminal amine on the polymer which can be used for further conjugation. This has allowed for not only fluorescent labeling of the polymer, but also protein......The field of drug delivery is in essence an exercise in engineered pharmacokinetics. Methods of doing so have been developed through the introduction of a vehicle carrying the drug, either by encapsulation or covalent attachment. The emergence of polymer therapeutics in anticancer therapy has...

  8. Polymer Fluid Dynamics. (United States)

    Bird, R. Byron


    Problems in polymer fluid dynamics are described, including development of constitutive equations, rheometry, kinetic theory, flow visualization, heat transfer studies, flows with phase change, two-phase flow, polymer unit operations, and drag reduction. (JN)

  9. Force signature of the unzipping transition for strip confined two-dimensional polymers (United States)

    Owczarek, Aleksander L.; Rechnitzer, Andrew


    We find and analyse the exact solution of two friendly walks, modelling polymers, confined between two parallel walls in a two-dimensional strip (or slit) where the polymers interact with each other via an attractive contact interaction. In the bulk, where the polymers are always far from any walls, there is an unzipping transition between phases where the two walks drift away for low attractive fugacity (high temperatures) and bind together for high attractive fugacities (low temperatures). Previously this has been used to model the denaturation of DNA. In a strip the transition is not sharp. However, we demonstrate that there is an abrupt change in the repulsive force exerted on the walls of the strip that can be calculated exactly. We suggest that this change in the force could be exploited to provide an experimental signature of the unzipping transition.

  10. Polymer dynamics from synthetic polymers to proteins

    Indian Academy of Sciences (India)

    Starting from the standard model of polymer motion - the Rouse model - we briefly present some key experimental results on the mesoscopic dynamics of polymer systems. We touch the role of topological confinement as expressed in the reptation model and discuss in some more detail processes limiting the confinement.

  11. Antimicrobial Modifications of Polymers


    Sedlarik, Vladimir


    This chapter is focused on antimicrobial modifications of polymer materials intended for medical devices production. Firstly, a brief introduction into the field of medical application of polymers is presented. Considering the fact that polymer medical devices are often connected with occurrence of nosocomial infections, the next part refers to this phenomenon and its causes. One of the possibilities of reducing of the infection occurrence is aimed at polymer modification. It is a key topic o...

  12. Microgel polymer composite fibres


    Kehren, Dominic


    In this thesis some novel ideas and advancements in the field of polymer composite fibres, specifically microgel-based polymer composite fibres have been achieved. The main task was to investigate and understand the electrospinning process of microgels and polymers and the interplay of parameter influences, in order to fabricate reproducible and continuously homogenous composite fibres. The main aim was to fabricate a composite material which combines the special properties of polymer fibres ...

  13. Amino Acid Bound Surfactants: A New Synthetic Family of Polymeric Monoliths Open Up Possibilities for Chiral Separations in Capillary Electrochromatography (United States)

    He, Jun; Wang, Xiaochun; Morrill, Mike; Shamsi, Shahab A.


    By combining a novel chiral amino-acid surfactant containing acryloyl amide tail, carbamate linker and leucine head group of different chain lengths with a conventional cross linker and a polymerization technique, a new “one-pot”, synthesis for the generation of amino-acid based polymeric monolith is realized. The method promises to open up the discovery of amino-acid based polymeric monolith for chiral separations in capillary electrochromatography (CEC). Possibility of enhanced chemoselectivity for simultaneous separation of ephedrine and pseudoephedrine containing multiple chiral centers, and the potential use of this amino-acid surfactant bound column for CEC and CEC coupled to mass spectrometric detection is demonstrated. PMID:22607448

  14. Modeling semiflexible polymer networks

    NARCIS (Netherlands)

    Broedersz, C.P.; MacKintosh, F.C.


    This is an overview of theoretical approaches to semiflexible polymers and their networks. Such semiflexible polymers have large bending rigidities that can compete with the entropic tendency of a chain to crumple up into a random coil. Many studies on semiflexible polymers and their assemblies have

  15. Structural and dynamical study about denatured states of yeast phosphoglycerate kinase by neutrons scattering and X-rays; Etude structurale et dynamique des etats denatures de la phosphoglycerate kinase de levure par diffusion des neutrons et des rayons X

    Energy Technology Data Exchange (ETDEWEB)

    Receveur, V


    During a long time, the neutron scattering and X-rays techniques have not been used for the studies bearing on the folding of proteins. The compactness and the globularness of a protein are two structural characteristics describing the denatured states and the intermediate states of folding, and the neutrons and x-rays scattering are probably the two techniques the most appropriate to give this kind of information; they are sensible to the spatial extent and to the molecules compactness, and to their general shape. For these three or four last years, the works using these techniques are increasing, giving precious knowledge on the different steps of folding and on the interactions stabilizing the denatured or intermediate states. This thesis falls into this category. (N.C.).

  16. Application of denaturing gradient gel electrophoresis (DGGE) for assessing fecal pollution sources at a recreational beach. (United States)

    Esseili, M A; Kassem, I I; Lis, J; Sigler, V


    We investigated the effectiveness of Escherichia coli community fingerprinting for identifying fecal pollution sources impacting a recreational beach. E. coli in water collected from the beach, nearby creek and storm sewer outfall were enumerated using membrane filtration, while E. coli communities were characterized following polymerase chain reaction analysis and denaturing gradient gel electrophoresis (DGGE) fingerprinting. Analysis of E. coli densities to determine the contributions of the creek and storm sewer during dry weather was inconclusive. However, DGGE fingerprinting indicated that the creek E. coli communities had a greater impact on the beach community composition (80-95% similarity), than on storm sewer communities (41-64%). Following rainfall events, E. coli communities in the creek were at least 93% similar to those at the beach, while the similarity of the outfall and beach communities varied from 72 to 96%. Furthermore, E. coli communities at the beach were more similar to creek communities than to storm sewer communities after the first 2 h and 48 h following the onset of rainfall, and of comparable similarity following 24 h of rainfall, suggesting transient contributions from the storm sewer. DGGE analysis of E. coli communities provided evidence that the creek was a consistent source of E. coli to the beach, while the storm sewer was a transient source.

  17. Inactivation, subunit dissociation, aggregation, and unfolding of myosin subfragment 1 during guanidine denaturation. (United States)

    Nozais, M; Béchet, J J; Houadjeto, M


    The effect of guanidine hydrochloride on ATPase activity, gel filtration, turbidity, exposure of thiol groups, far-UV circular dichroism, and the fluorescence emission intensity of myosin subfragment 1 (S-1) was studied under equilibrium conditions. It was found that the denaturation process involves several intermediate states. The enzymatic activity of S-1 is at first lost at very low concentrations of GdnHCl (lower than 0.5 M). At a slightly higher GdnHCl concentration (about 0.5 M), the light chains dissociate and this dissociation is closely followed by the formation of aggregates between the naked heavy chains of S-1 molecules in the guanidine hydrochloride range of concentrations 0.5-1 M. At GdnHCl concentrations above 1 M, aggregates gradually disappear and S-1 loses its secondary and tertiary structures. These phenomena are partly reversible, and ATPase activity is only partially recovered under highly limited conditions. These results are discussed in relation to the nature of myosin subunit assembly. The head fragment of 20 kDa is thus suggested to be implicated in the binding of light chain to heavy chain and in the self-association of free heavy chains.

  18. Formation of Polyphenol-Denatured Protein Flocs in Alcohol Beverages Sweetened with Refined Cane Sugars. (United States)

    Eggleston, Gillian; Triplett, Alexa


    The sporadic appearance of floc from refined, white cane sugars in alcohol beverages remains a technical problem for both beverage manufacturers and sugar refiners. Cane invert sugars mixed with 60% pure alcohol and water increased light scattering by up to ∼1000-fold. Insoluble and soluble starch, fat, inorganic ash, oligosaccharides, Brix, and pH were not involved in the prevailing floc-formation mechanism. Strong polynomial correlations existed between the haze floc and indicator values (IVs) (color at 420 nm pH 9.0/color at pH 4.0-an indirect measure of polyphenolic and flavonoid colorants) (R 2 = 0.815) and protein (R 2 = 0.819) content of the invert sugars. Ethanol-induced denaturation of the protein exposed hydrophobic polyphenol-binding sites that were further exposed when heated to 80 °C. A tentative mechanism for floc formation was advanced by molecular probing with a haze (floc) active protein and polyphenol as well as polar, nonpolar, and ionic solvents.

  19. Size distribution of DNA molecules recovered from non-denaturing filter elution

    International Nuclear Information System (INIS)

    Bloecher, D.; Iliakis, G.


    DNA fragments removed from the filter during non-denaturing filter elution were collected and loaded on top of neutral sucrose gradients. Their size distribution was determined by low-speed centrifugation in neutral sucrose gradients. The average size of eluted DNA was found to be approximately 110 S; the average size of DNA collected after short elution times was found to be slightly larger than after long elution times. It is concluded that the size of eluted DNA fragments is not correlated with elution rate, and it is proposed that shear forces generated at the filter pores cause degradation of the DNA. Comparison of sedimentation profiles of carefully prepared cellular DNA before and after elution revealed that generated shear forces during elution break down DNA to an extent equivalent to around 20 000 DNA double-strand breaks (dsb) per G 1 cell. The size of DNA fragments decreased with increasing radiation dose; five times more dsb were found than expected after exposure to radiation alone. It is proposed that excess of dsb may derive from the transformation of other radiation-induced lesions to dsb under the action of shear forces generated during elution. (author)

  20. Precise determination of protein extinction coefficients under native and denaturing conditions using SV-AUC. (United States)

    Hoffmann, Andreas; Grassl, Kerstin; Gommert, Janine; Schlesak, Christian; Bepperling, Alexander


    The accurate determination of protein concentration is an important though non-trivial task during the development of a biopharmaceutical. The fundamental prerequisite for this is the availability of an accurate extinction coefficient. Common approaches for the determination of an extinction coefficient for a given protein are either based on the theoretical prediction utilizing the amino acid sequence or the photometric determination combined with a measurement of absolute protein concentration. Here, we report on an improved SV-AUC based method utilizing an analytical ultracentrifuge equipped with absorbance and Rayleigh interference optics. Global fitting of datasets helped to overcome some of the obstacles encountered with the traditional method employing synthetic boundary cells. Careful calculation of dn/dc values taking glycosylation and solvent composition into account allowed the determination of the extinction coefficients of monoclonal antibodies and an Fc-fusion protein under native as well as under denaturing conditions. An intra-assay precision of 0.9% and an accuracy of 1.8% compared to the theoretical value was achieved for monoclonal antibodies. Due to the large number of data points of a single dataset, no meaningful difference between the ProteomeLab XL-I and the new Optima AUC platform could be observed. Thus, the AUC-based approach offers a precise, convenient and versatile alternative to conventional methods like total amino acid analysis (AAA).

  1. Peptide biosensors for anticancer drugs: Design in silico to work in denaturizing environment. (United States)

    Guida, Filomena; Battisti, Anna; Gladich, Ivan; Buzzo, Mauro; Marangon, Elena; Giodini, Luciana; Toffoli, Giuseppe; Laio, Alessandro; Berti, Federico


    One of the main targets in current clinical oncology is the development of a cheap device capable of monitoring in real-time the concentration of a drug in the blood of a patient. This would allow fine-tuning the dosage according to the patient's metabolism, a key condition to reduce side effects. By using surface plasmon resonance and fluorescence spectroscopy we here show that short peptides designed in silico by a recently developed algorithm are capable of binding the anticancer drug irinotecan (CPT-11) with micromolar affinity. Importantly, the recognition takes place in the denaturating solution used in standard therapeutic drug monitoring to detach the drug from the proteins that are present in human plasma, and some of the peptides are capable of distinguishing CPT-11 from its metabolite SN-38. These results suggest that the in silico design of small artificial peptides is now a viable route for designing sensing units, opening a wide range of applications in diagnostic and clinical areas. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. [Study on the use of haemoglobin denaturation test as an alternative to Draize eye irritation test]. (United States)

    Liao, Yan; Wang, Xue; Zhang, Li-shi; Li, Guan-min; Zhang, Bao-xu


    To use haemoglobin denaturation test (HD test) as an alternative to Draize eye irritation test (Draize test). Fourteen cosmetic ingredients were tested by HD test. The results were compared with two kinds of scores in Draize test, i.e. Maximum average Draize total score (MAS) and Score of 24 h after application (S24). The correlation coefficient between RDC50 and MAS and that between RDC50 and S24 were 0.926 and 0.921 respectively, while that between 1%lambdamax and MAS, and between 1%lambdamax and S24 were 0.881 and 0.791 respectively. The results showed that RDC50 had a higher correlation with Draize test than 1%lambdamax did, but in the use of RDC50 some information of data would be lost. On the other hand, 1%lambdamax, which had a greater correlation with corneal score in the three component scores of the Draize test, could be used for assessing water-insoluble chemicals. The results showed that HD test could be used as an effective alternative to Draize eye irritation test.

  3. Backbone Dynamics of the Monomeric λ Repressor Denatured State Ensemble under Nondenaturing Conditions† (United States)

    Chugha, Preeti; Oas, Terrence G.


    Oxidizing two native methionine residues predominantly populates the denatured state of monomeric λ repressor (MetO-λLS) under nondenaturing conditions. NMR was used to characterize the secondary structure and dynamics of MetO-λLS in standard phosphate buffer. 13Cα and 1Hα chemical shift indices reveal a region of significant helicity between residues 9 and 29. This helical content is further supported by the observation of medium-range amide NOEs. The remaining residues do not exhibit significant helicity as determined by NMR. We determined 15N relaxation parameters for 64 of 85 residues at 600 and 800 MHz. There are two distinct regions of reduced flexibility, residues 8–32 in the N-terminal third and residues 50–83 in the C-terminal third. The middle third, residues 33–50, has greater flexibility. We have analyzed the amplitude of the backbone motions in terms of the physical properties of the amino acids and conclude that conformational restriction of the backbone MetO-λLS is due to nascent helix formation in the region corresponding to native helix 1. The bulkiness of amino acid residues in the C-terminal third leads to the potential for hydrophobic interactions, which is suggested by chemical exchange detected by the difference in spectral density J(0) at the two static magnetic fields. The more flexible middle region is the result of a predominance of small side chains in this region. PMID:17260944

  4. Environmental-induced acquisition of nuptial plumage expression: a role of denaturation of feather carotenoproteins? (United States)

    Blanco, Guillermo; Frías, Oscar; Garrido-Fernández, Juan; Hornero-Méndez, Dámaso


    Several avian species show a bright carotenoid-based coloration during spring and following a period of duller coloration during the previous winter, despite carotenoids presumably being fully deposited in feathers during the autumn moult. Carotenoid-based breast feathers of male linnets (Carduelis cannabina) increased in hue (redness), saturation and brightness after exposing them to outdoor conditions from winter to spring. This represents the first experimental evidence showing that carotenoid-based plumage coloration may increase towards a colourful expression due to biotic or abiotic environmental factors acting directly on full-grown feathers when carotenoids may be fully functional. Sunlight ultraviolet (UV) irradiation was hypothesized to denature keratin and other proteins that might protect pigments from degradation by this and other environmental factors, suggesting that sunlight UV irradiation is a major factor in the colour increase from winter to spring. Feather proteins and other binding molecules, if existing in the follicles, may be linked to carotenoids since their deposition into feathers to protect colourful features of associated carotenoids during the non-breeding season when its main signalling function may be relaxed. Progress towards uncovering the significance of concealment and subsequent display of colour expression should consider the potential binding and protecting nature of feather proteins associated with carotenoids. PMID:16191594

  5. Protein denaturation of whey protein isolates (WPIs) induced by high intensity ultrasound during heat gelation. (United States)

    Frydenberg, Rikke P; Hammershøj, Marianne; Andersen, Ulf; Greve, Marie T; Wiking, Lars


    In this study, the impact of high intensity ultrasound (HIU) on proteins in whey protein isolates was examined. Effects on thermal behavior, secondary structure and nature of intra- and intermolecular bonds during heat-induced gelling were investigated. Ultrasonication (24 kHz, 300 W/cm(2), 2078 J/mL) significantly reduced denaturation enthalpies, whereas no change in secondary structure was detected by circular dichroism. The thiol-blocking agent N-ethylmaleimide was applied in order to inhibit formation of disulfide bonds during gel formation. Results showed that increased contents of α-lactalbumin (α-La) were associated with increased sensitivity to ultrasonication. The α-La:β-lactoglobulin (β-Lg) ratio greatly affected the nature of the interactions formed during gelation, where higher amounts of α-La lead to a gel more dependent on disulfide bonds. These results contribute to clarifying the mechanisms mediating the effects of HIU on whey proteins on the molecular level, thus moving further toward implementing HIU in the processing chain in the food industry. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Potential use of gradient denaturing gel electrophoresis in obtaining mutational spectra from human cells

    International Nuclear Information System (INIS)

    Thilly, W.G.


    A method is described to isolate mutations in DNA in human cells. When a double-stranded DNA migrates through an electric field on an electrophoretic gel, it is compact hydrodynamic structure relative to the same material in a melted form. Normally the solution in electrophoretic gels is uniform, but a way has been devised to set up a stable gradient of increasing solute concentration in the direction of DNA motion. Thus, as a double-stranded DNA molecule is drawn by the electric field into higher and higher concentrations of urea/formamide, it will eventually reach a point at which the concentration is high enough to melt the lower-melting-point region. The melting results in an essentially immobile structure within the gel so that the position at which the DNA molecule stops on the gradient gel is determined by its melting point, which is uniquely determined by its nucleotide sequence. A single base pair substitution within a low melting point sequence of some 100 base pairs changed the expected melting point by 0.4 0 C and resulted in about a 2-cm displacement under appropriate denaturing gel conditions. This expectation leads to the idea that if a mixture of DNA sequences derived from point mutations within the same restriction fragment were permitted to anneal with a complementary wild-type sequence, the melting point of each type of heteroduplex would differ depending on the kind and position of each mutation

  7. The Effect of Elasticityon the Extrudate Swell of Molten Polymers (United States)

    Hatzikiriakos, Savvas; Konaganti, Vinod Kumar; UBC Team


    The extrudate swell of an industrial grade high molecular weight high-density polyethylene (HDPE) in capillary dies is studied using the integral K-BKZ constitutive model. The non-linear viscoelastic flow properties of the polymer resin are studied for a broad range of large step shear strains and high shear rates using the cone partitioned plate (CPP) geometry of the stress/strain controlled rotational rheometer. This allowed the determination of the rheological parameters accurately, in particular the damping function, which is proven to be the most important in simulating transient flows such as extrudate swell. A series of simulations performed using the integral K-BKZ Wagner model with different values of the Wagner exponent n, ranging from n = 0.15 to 0.5, demonstrates that the extrudate swell predictions are extremely sensitive to the Wagner damping function exponent. Using the correct n - value resulted in extrudate swell predictions that are in excellent agreement with experimental measurements. .

  8. Electroluminescence of Multicomponent Conjugated Polymers. 1. Roles of Polymer/Polymer Interfaces in Emission Enhancement and Voltage-Tunable Multicolor Emission in Semiconducting Polymer/Polymer Heterojunctions

    National Research Council Canada - National Science Library

    Zhang, Xuejun, Ph.D


    Effects of the electronic structure of polymer/polymer interfaces on the electroluminescence efficiency and tunable multicolor emission of polymer heterojunction light-emitting diodes were explored...

  9. Nanoporous polymer electrolyte (United States)

    Elliott, Brian [Wheat Ridge, CO; Nguyen, Vinh [Wheat Ridge, CO


    A nanoporous polymer electrolyte and methods for making the polymer electrolyte are disclosed. The polymer electrolyte comprises a crosslinked self-assembly of a polymerizable salt surfactant, wherein the crosslinked self-assembly includes nanopores and wherein the crosslinked self-assembly has a conductivity of at least 1.0.times.10.sup.-6 S/cm at C. The method of making a polymer electrolyte comprises providing a polymerizable salt surfactant. The method further comprises crosslinking the polymerizable salt surfactant to form a nanoporous polymer electrolyte.

  10. Radiation effects on polymers

    International Nuclear Information System (INIS)

    Clough, R.L.; Shalaby, S.W.


    This book covers polymer radiation effects to be available in more than a decade. This volume reviews the fundamental chemistry and physics of polymer-radiation interaction and examines recent progress in most major areas of the field. Its 38 chapters, cover: fundamentals of polymer radiation chemistry; technological applications of radiation to polymers (including radiation processing; radiation curing; sterilization; cross-linking, polymerization, grafting, x-ray resists, and others); and degradation of stabilization of irradiated polymers (including nuclear plants, scintillation detectors for particle physics, and others)

  11. Biostable glucose permeable polymer

    DEFF Research Database (Denmark)


    A new biostable glucose permeable polymer has been developed which is useful, for example, in implantable glucose sensors. This biostable glucose permeable polymer has a number of advantageous characteristics and, for example, does not undergo hydrolytic cleavage and degradation, thereby providing...... a composition that facilitates long term sensor stability in vivo. The versatile characteristics of this polymer allow it to be used in a variety of contexts, for example to form the body of an implantable glucose sensor. The invention includes the polymer composition, sensor systems formed from this polymer...

  12. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  13. Fourier Transformation Analysis in Capillary Flow—A New Option to Detect Flow Instabilities (Shark Skin) (United States)

    Sunder, Joachim


    Flow instabilities cause various problems in extrusion blow- or flat film processes. Especially shark skin is affected by molecular structure. This phenomenon is analyzed in various scientific works using apparatus that are complex or difficult in operation. A new set-up, now available is being presented as an option for new and existing capillary rheometers or lab extruders, consisting of a special designed die, a fast responsive transducers system and evaluation software. The software allows the evaluation of diverse pressure frequency regimes causing flow instabilities and generate statistics. Measurement examples are given for different shear rates and polymers. The shark skin effect can be detected even before it is visible on the extrudate. The measured frequency regimes are related to molecular parameters.

  14. A Comparison Between Denaturing Gradient Gel Electrophoresis and Denaturing High Performance Liquid Chromatography in Detecting Mutations in Genes Associated with Hereditary Non-Polyposis Colorectal Cancer (HNPCC and the Identification of 9 New Mutations Previously Unidentified by DGGE

    Directory of Open Access Journals (Sweden)

    Meldrum Cliff J


    Full Text Available Abstract Denaturing high performance liquid chromatography is a relatively new method by which heteroduplex structures formed during the PCR amplification of heterozygote samples can be rapidly identified. The use of this technology for mutation detection in hereditary non-polyposis colorectal cancer (HNPCC has the potential to appreciably shorten the time it takes to analyze genes associated with this disorder. Prior to acceptance of this method for screening genes associated with HNPCC, assessment of the reliability of this method should be performed. In this report we have compared mutation and polymorphism detection by denaturing gradient gel electrophoresis (DGGE with denaturing high performance liquid chromatography (DHPLC in a set of 130 families. All mutations/polymorphisms representing base substitutions, deletions, insertions and a 23 base pair inversion were detected by DHPLC whereas DGGE failed to identify four single base substitutions and a single base pair deletion. In addition, we show that DHPLC has been used for the identification of 5 different mutations in exon 7 of hMSH2 that could not be detected by DGGE. From this study we conclude that DHPLC is a more effective and rapid alternative to the detection of mutations in hMSH2 and hMLH1 with the same or better accuracy than DGGE. Furthermore, this technique offers opportunities for automation, which have not been realised for the majority of other methods of gene analysis.

  15. Fluorination of polymers

    International Nuclear Information System (INIS)

    Du Toit, F.J.


    Polyethylene and polypropylene were reacted with elemental fluorine under carefully controlled conditions to produce fluorocarbon polymers. Fluorination of polymer films resulted in fluorination of only the outer surfaces of the films, while the reaction of elemental fluorine with powdered hydrocarbon polymers produced perfluorocarbon polymers. Existing and newly developed techniques were used to characterize the fluorinated polymers. It was shown that the degree of fluorination was influenced by the surface area of the hydrocarbon material, the concentration, of the fluorine gas, and the time and temperature of fluorination. A fluidized-bed reactor used for the fluorination of polymer powders effectively increased the reaction rate. The surface tension and the oxygen permeability of the fluorinated polymers were studied. The surface tension of hydrocarbon polymers was not influenced by different solvents, but the surface tension of fluorinated polymers was affected by the type of solvent that was used. There were indications that the surface tension was affected by oxygen introduced into the polymer surface during fluorination. Fluorination lowered the permeability of oxygen through hydrocarbon polymers. 55 refs., 51 figs., 26 tabs

  16. In-capillary approach to eliminate SDS interferences in antibody analysis by capillary electrophoresis coupled to mass spectrometry. (United States)

    Sánchez-Hernández, Laura; Montealegre, Cristina; Kiessig, Steffen; Moritz, Bernd; Neusüß, Christian


    Capillary electrophoresis is an important technique for the characterization of monoclonal antibodies (mAbs), especially in the pharmaceutical context. However, identification is difficult as upscaling and hyphenation of used methods directly to mass spectrometry is often not possible due to separation medium components that are incompatible with MS detection. Here a CE-MS method for the analysis of mAbs is presented analyzing SDS-complexed samples. To obtain narrow and intensive peaks of SDS-treated antibodies, an in-capillary strategy was developed based on the co-injection of positively charged surfactants and methanol as organic solvent. For samples containing 0.2% (v/v) of SDS, recovered MS peak intensities up to 97 and 95% were achieved using cetyltrimethylammonium bromide or benzalkonium chloride, respectively. Successful removal of SDS was shown in neutral coated capillaries but also in a capillary with a positively charged coating applying reversed polarity. The usefulness of this in-capillary strategy was demonstrated also for other proteins and for antibodies dissolved in up to 10% v/v SDS solution, and in other SDS-containing matrices, including the sieving matrix used in a standard CE-SDS method and gel-buffers applied in SDS-PAGE methods. The developed CE-MS approaches enable fast and reproducible characterization of SDS-complexed antibodies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Sensitivity enhancement in near-field photothermal-lens detection in capillary electrophoresis using laser-induced online precipitation. (United States)

    Nedosekin, Dmitry A; Faubel, Werner; Proskurnin, Mikhail A; Pyell, Ute


    This paper reports simultaneous photoinduced precipitation-based online preconcentration of target analytes at the inner walls in capillary zone electrophoresis (CZE) and surface-enhanced near-field crossed-beam photothermal-lens detection of the preconcentrated analytes. A simple technique using online readjustment of the optical scheme of the thermal-lens detector in the course of the separation for gaining optimum sensitivity for both water-soluble and precipitated analytes is proposed. It provides a considerable decrease in the limits of detection (LOD) with good concordance with the previously developed theoretical approach to this combination (D. A. Nedosekin, W. Faubel, M. A. Proskurnin, and U. Pyell, Talanta, 78, 682-690 (2009)). As a result, an enhancement of more than an order of magnitude in the limit of detection of the photoactive 4-aminoazobenzene compared to conventional thermal-lens detection in CZE is achieved while retaining very good sensitivity for unabsorbed analyte (Mordant Yellow 7). The application of the thermal-lens detector to the investigation of laser-induced reactions in flow in capillaries is discussed.

  18. Advanced polymers in medicine

    CERN Document Server

    Puoci, Francesco


    The book provides an up-to-date overview of the diverse medical applications of advanced polymers. The book opens by presenting important background information on polymer chemistry and physicochemical characterization of polymers. This serves as essential scientific support for the subsequent chapters, each of which is devoted to the applications of polymers in a particular medical specialty. The coverage is broad, encompassing orthopedics, ophthalmology, tissue engineering, surgery, dentistry, oncology, drug delivery, nephrology, wound dressing and healing, and cardiology. The development of polymers that enhance the biocompatibility of blood-contacting medical devices and the incorporation of polymers within biosensors are also addressed. This book is an excellent guide to the recent advances in polymeric biomaterials and bridges the gap between the research literature and standard textbooks on the applications of polymers in medicine.

  19. Simultaneous immobilization of dehydrogenases on polyvinylidene difluoride resin after separation by non-denaturing two-dimensional electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Shimazaki, Youji [Graduate School of Science and Engineering (Science Section) and Venture Business Laboratory, Ehime University, Bunkyo-cho 2-5, Matsuyama City 790-8577 (Japan)], E-mail:; Kadota, Mariko [Faculty of Science, Ehime University, Matsuyama (Japan)


    We detected mouse liver malate, sorbitol and aldehyde dehydrogenases by negative staining, analysis of malate and sorbitol dehydrogenase activities using each substrate, and electron transfers including nicotinamide adenine dinucleotide (NAD) and nitroblue tetrazolium in non-denaturing two-dimensional electrophoresis (2-DE) gel. Dehydrogenases were also identified by electrospray ionization tandem mass spectrometry (ESI-MS/MS) after 2-DE separation and protein detection by negative staining. Spots of dehydrogenases separated by 2-DE were excised, and simultaneously transferred and immobilized on polyvinylidene difuoride (PVDF) resin by electrophoresis. The dehydrogenase activities remained intact after immobilization. In conclusion, resin-immobilized dehydrogenases can be simultaneously obtained after separation by non-denaturing 2-DE, detection by negative staining and transferring to resins.

  20. Structural and dynamical study about denatured states of yeast phosphoglycerate kinase by neutrons scattering and X-rays

    International Nuclear Information System (INIS)

    Receveur, V.


    During a long time, the neutron scattering and X-rays techniques have not been used for the studies bearing on the folding of proteins. The compactness and the globularness of a protein are two structural characteristics describing the denatured states and the intermediate states of folding, and the neutrons and x-rays scattering are probably the two techniques the most appropriate to give this kind of information; they are sensible to the spatial extent and to the molecules compactness, and to their general shape. For these three or four last years, the works using these techniques are increasing, giving precious knowledge on the different steps of folding and on the interactions stabilizing the denatured or intermediate states. This thesis falls into this category. (N.C.)

  1. The regulatory subunit of PKA-I remains partially structured and undergoes β-aggregation upon thermal denaturation.

    Directory of Open Access Journals (Sweden)

    Khanh K Dao

    Full Text Available BACKGROUND: The regulatory subunit (R of cAMP-dependent protein kinase (PKA is a modular flexible protein that responds with large conformational changes to the binding of the effector cAMP. Considering its highly dynamic nature, the protein is rather stable. We studied the thermal denaturation of full-length RIα and a truncated RIα(92-381 that contains the tandem cyclic nucleotide binding (CNB domains A and B. METHODOLOGY/PRINCIPAL FINDINGS: As revealed by circular dichroism (CD and differential scanning calorimetry, both RIα proteins contain significant residual structure in the heat-denatured state. As evidenced by CD, the predominantly α-helical spectrum at 25°C with double negative peaks at 209 and 222 nm changes to a spectrum with a single negative peak at 212-216 nm, characteristic of β-structure. A similar α→β transition occurs at higher temperature in the presence of cAMP. Thioflavin T fluorescence and atomic force microscopy studies support the notion that the structural transition is associated with cross-β-intermolecular aggregation and formation of non-fibrillar oligomers. CONCLUSIONS/SIGNIFICANCE: Thermal denaturation of RIα leads to partial loss of native packing with exposure of aggregation-prone motifs, such as the B' helices in the phosphate-binding cassettes of both CNB domains. The topology of the β-sandwiches in these domains favors inter-molecular β-aggregation, which is suppressed in the ligand-bound states of RIα under physiological conditions. Moreover, our results reveal that the CNB domains persist as structural cores through heat-denaturation.

  2. Use of Denaturing High-Performance Liquid Chromatography for Rapid Detection and Identification of Seven Candida Species


    Goldenberg, Oliver; Herrmann, Stefanie; Adam, Thomas; Marjoram, Gina; Hong, George; Göbel, Ulf B.; Graf, Barbara


    A novel denaturing high-performance liquid chromatography (DHPLC)-based technique allows rapid high-resolution analysis of PCR products. We used this technique for unequivocal molecular identification of seven Candida species. We show the application of this PCR/DHPLC approach for direct detection and identification of yeast species from blood cultures and for detection of Candida colonization in the gastrointestinal tract of allogeneic transplant patients.

  3. Acid-denatured Green Fluorescent Protein (GFP) as model substrate to study the chaperone activity of protein disulfide isomerase. (United States)

    Mares, Rosa E; Meléndez-López, Samuel G; Ramos, Marco A


    Green fluorescent protein (GFP) has been widely used in several molecular and cellular biology applications, since it is remarkably stable in vitro and in vivo. Interestingly, native GFP is resistant to the most common chemical denaturants; however, a low fluorescence signal has been observed after acid-induced denaturation. Furthermore, this acid-denatured GFP has been used as substrate in studies of the folding activity of some bacterial chaperones and other chaperone-like molecules. Protein disulfide isomerase enzymes, a family of eukaryotic oxidoreductases that catalyze the oxidation and isomerization of disulfide bonds in nascent polypeptides, play a key role in protein folding and it could display chaperone activity. However, contrasting results have been reported using different proteins as model substrates. Here, we report the further application of GFP as a model substrate to study the chaperone activity of protein disulfide isomerase (PDI) enzymes. Since refolding of acid-denatured GFP can be easily and directly monitored, a simple micro-assay was used to study the effect of the molecular participants in protein refolding assisted by PDI. Additionally, the effect of a well-known inhibitor of PDI chaperone activity was also analyzed. Because of the diversity their functional activities, PDI enzymes are potentially interesting drug targets. Since PDI may be implicated in the protection of cells against ER stress, including cancer cells, inhibitors of PDI might be able to enhance the efficacy of cancer chemotherapy; furthermore, it has been demonstrated that blocking the reductive cleavage of disulfide bonds of proteins associated with the cell surface markedly reduces the infectivity of the human immunodeficiency virus. Although several high-throughput screening (HTS) assays to test PDI reductase activity have been described, we report here a novel and simple micro-assay to test the chaperone activity of PDI enzymes, which is amenable for HTS of PDI

  4. Mercury(II) binds to both of chymotrypsin's histidines, causing inhibition followed by irreversible denaturation/aggregation. (United States)

    Stratton, Amanda; Ericksen, Matthew; Harris, Travis V; Symmonds, Nick; Silverstein, Todd P


    The toxicity of mercury is often attributed to its tight binding to cysteine thiolate anions in vital enzymes. To test our hypothesis that Hg(II) binding to histidine could be a significant factor in mercury's toxic effects, we studied the enzyme chymotrypsin, which lacks free cysteine thiols; we found that chymotrypsin is not only inhibited, but also denatured by Hg(II). We followed the aggregation of denatured enzyme by the increase in visible absorbance due to light scattering. Hg(II)-induced chymotrypsin precipitation increased dramatically above pH 6.5, and free imidazole inhibited this precipitation, implicating histidine-Hg(II) binding in the process of chymotrypsin denaturation/aggregation. Diethylpyrocarbonate (DEPC) blocked chymotrypsin's two histidines (his 40 and his 57 ) quickly and completely, with an IC 50 of 35 ± 6 µM. DEPC at 350 µM reduced the hydrolytic activity of chymotrypsin by 90%, suggesting that low concentrations of DEPC react with his 57 at the active site catalytic triad; furthermore, DEPC below 400 µM enhanced the Hg(II)-induced precipitation of chymotrypsin. We conclude that his 57 reacts readily with DEPC, causing enzyme inhibition and enhancement of Hg(II)-induced aggregation. Above 500 µM, DEPC inhibited Hg(II)-induced precipitation, and [DEPC] >2.5 mM completely protected chymotrypsin against precipitation. This suggests that his 40 reacts less readily with DEPC, and that chymotrypsin denaturation is caused by Hg(II) binding specifically to the his 40 residue. Finally, we show that Hg(II)-histidine binding may trigger hemoglobin aggregation as well. Because of results with these two enzymes, we suggest that metal-histidine binding may be key to understanding all heavy metal-induced protein aggregation. © 2017 The Protein Society.

  5. Definition of the native and denatured type II collagen binding site for fibronectin using a recombinant collagen system. (United States)

    An, Bo; Abbonante, Vittorio; Yigit, Sezin; Balduini, Alessandra; Kaplan, David L; Brodsky, Barbara


    Interaction of collagen with fibronectin is important for extracellular matrix assembly and regulation of cellular processes. A fibronectin-binding region in collagen was identified using unfolded fragments, but it is not clear if the native protein binds fibronectin with the same primary sequence. A recombinant bacterial collagen is utilized to characterize the sequence requirement for fibronectin binding. Chimeric collagens were generated by inserting the putative fibronectin-binding region from human collagen into the bacterial collagen sequence. Insertion of a sufficient length of human sequence conferred fibronectin affinity. The minimum sequence requirement was identified as a 6-triplet sequence near the unique collagenase cleavage site and was the same in both triple-helix and denatured states. Denaturation of the chimeric collagen increased its affinity for fibronectin, as seen for mammalian collagens. The fibronectin binding recombinant collagen did not contain hydroxyproline, indicating hydroxyproline is not essential for binding. However, its absence may account, in part, for the higher affinity of the native chimeric protein and the lower affinity of the denatured protein compared with type II collagen. Megakaryocytes cultured on chimeric collagen with fibronectin affinity showed improved adhesion and differentiation, suggesting a strategy for generating bioactive materials in biomedical applications.

  6. A Proposed Mechanism for the Thermal Denaturation of a Recombinant Bacillus Halmapalus Alpha-amylase - the Effect of Calcium Ions (United States)

    Nielsen, Anders D.; Pusey, Marc L.; Fuglsang, Claus C.; Westh, Peter


    The thermal stability of a recombinant alpha-amylase from Bacillus halmapalus alpha-amylase (BHA) has been investigated using circular dichroism spectroscopy (CD) and differential scanning calorimetry (DSC). This alpha-amylase is homologous to other Bacillus alpha-amylases where previous crystallographic studies have identified the existence of 3 calcium binding sites in the structure. Denaturation of BHA is irreversible with a Tm of approximately 89 C, and DSC thermograms can be described using a one-step irreversible model. A 5 C increase in T(sub m) in the presence of 10 fold excess CaCl2 was observed. However, a concomitant increase in the tendency to aggregate was also observed. The presence of 30-40 fold excess calcium chelator (EDTA or EGTA) results in a large destabilization of BHA corresponding to about 40 C lower T(sub m), as determined by both CD and DSC. Ten fold excess EGTA reveals complex DSC thermograms corresponding to both reversible and irreversible transitions, which possibly originate from different populations of BHA:calcium complexes. The observations in the present study have, in combination with structural information of homologous alpha-amylases, provided the basis for the proposal of a simple denaturation mechanism of BHA. The proposed mechanism describes the irreversible thermal denaturation of different BHA:calcium complexes and the calcium binding equilibrium involved. Furthermore, the model accounts for a temperature induced reversible structural change associated with calcium binding.

  7. Selection for Protein Kinetic Stability Connects Denaturation Temperatures to Organismal Temperatures and Provides Clues to Archaean Life (United States)

    Romero-Romero, M. Luisa; Risso, Valeria A.; Martinez-Rodriguez, Sergio; Gaucher, Eric A.; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.


    The relationship between the denaturation temperatures of proteins (Tm values) and the living temperatures of their host organisms (environmental temperatures: TENV values) is poorly understood. Since different proteins in the same organism may show widely different Tm’s, no simple universal relationship between Tm and TENV should hold, other than Tm≥TENV. Yet, when analyzing a set of homologous proteins from different hosts, Tm’s are oftentimes found to correlate with TENV’s but this correlation is shifted upward on the Tm axis. Supporting this trend, we recently reported Tm’s for resurrected Precambrian thioredoxins that mirror a proposed environmental cooling over long geological time, while remaining a shocking ~50°C above the proposed ancestral ocean temperatures. Here, we show that natural selection for protein kinetic stability (denaturation rate) can produce a Tm↔TENV correlation with a large upward shift in Tm. A model for protein stability evolution suggests a link between the Tm shift and the in vivo lifetime of a protein and, more specifically, allows us to estimate ancestral environmental temperatures from experimental denaturation rates for resurrected Precambrian thioredoxins. The TENV values thus obtained match the proposed ancestral ocean cooling, support comparatively high Archaean temperatures, and are consistent with a recent proposal for the environmental temperature (above 75°C) that hosted the last universal common ancestor. More generally, this work provides a framework for understanding how features of protein stability reflect the environmental temperatures of the host organisms. PMID:27253436

  8. High Intensity Focused Ultrasound Monitoring using Harmonic Motion Imaging for Focused Ultrasound (HMIFU) under boiling or slow denaturation conditions (United States)

    Hou, Gary Y.; Marquet, Fabrice; Wang, Shutao; Apostolakis, Iason-Zacharias; Konofagou, Elisa E.


    Harmonic Motion Imaging for Focused Ultrasound (HMIFU) is a recently developed High-Intensity Focused Ultrasound (HIFU) treatment monitoring method that utilizes an amplitude-modulated therapeutic ultrasound beam to induce an oscillatory radiation force at the HIFU focus and estimates the focal tissue displacement to monitor the HIFU thermal treatment. In this study, the performance of HMIFU under acoustic, thermal and mechanical effects were investigated. The performance of HMIFU was assessed in ex vivo canine liver specimens (n=13) under slow denaturation or boiling regimes. Passive Cavitation Detector (PCD) was used to assess the acoustic cavitation activity while a bare-wire thermocouple was used to monitor the focal temperature change. During lesioning with slow denaturation, high quality displacements (correlation coefficient above 0.97) were observed under minimum cavitation noise, indicating tissue the initial-softening-then-stiffening property change. During HIFU with boiling, HMIFU monitored a consistent change in lesion-to-background displacement contrast (0.46±0.37) despite the presence of strong cavitation noise due to boiling during lesion formation. Therefore, HMIFU effectively monitored softening-then-stiffening during lesioning under slow denaturation, and detected lesioning under boiling with a distinct change in displacement contrast under boiling in the presence of cavitation. In conclusion, HMIFU was shown effective in HIFU monitoring and lesioning identification without being significantly affected by cavitation noise. PMID:26168177

  9. Preparation of denatured protein bone sterilized with gamma radiation; Preparacion de hueso desproteinizado esterilizado con radiacion gamma

    Energy Technology Data Exchange (ETDEWEB)

    Luna Z, D. [ININ, 52045 Ocoyoacac, Estado de Mexico (Mexico)]. e-mail:


    The bone is one of the tissues more transplanted in the entire world by that the bone necessity for transplant every day becomes bigger. In the Bank of tissues Radio sterilized of the ININ the amnion and the pig skin are routinely processed. The tissue with which will be continued is with bone. Due to that in our country it doesn't have enough bone of human origin for the necessities required in the bone transplant, an option is the bone of bovine. Of this bone one can obtain denatured protein bone, with the same characteristics of the denatured protein human bone, the one which has been proven that it has good acceptance and incorporation in the human body when is transplanted. The method for the obtaining of the denatured protein bone of bovine, with the confirmation of the final product by means of X-ray diffraction is described. The radiosterilization of this bone with gamma rays and the determination of the lead content. (Author)

  10. Acid and thermal denaturation of barnase investigated by molecular dynamics simulations. (United States)

    Caflisch, A; Karplus, M


    The transition in barnase from the native state to a partially unfolded conformation has been studied by molecular dynamics simulations with explicit water molecules at 360 K and low pH(450 ps), and at 600 K and neutral pH (three simulations of 120, 250 and 200 ps each). The use of several simulations provides evidence that the results are not sensitive to initial conditions. To mimic low pH conditions, the acidic sidechains in barnase were neutralized and the two histidine residues were doubly protonated. Runs at 300 K showed that the solvated structures at low pH (300 ps) and neutral pH (310 ps) are very similar. The main structural differences involved the acidic residues, histidine residues, and the beta-turn connecting strands 4 and 5. When the temperature is raised to 360 K at low pH and to 600 K at neutral pH the barnase molecule begins to unfold. The molecule rapidly expands (Rg changes from 13.9 A to 15.3 A in 450 ps at 360 K and from 13.7 A to between 15.1 and 15.5 A in 120 ps at 600 K). However, the expansion is not uniform. In all the simulations, the chain termini, loops and the N-terminal parts of the main alpha-helix (helix 1) show a continuous and progressive unfolding. An essential step in the denaturation process is that the major alpha-helix (helix 1) separates from the beta-sheet; this is coupled to the exposure of the principal hydrophobic core, many of whose non-polar side chains become solvated by hydrogen-bonded water molecules. The barnase-water interaction energy improves during unfolding at the expense of the barnase self-energy. The deterioration of the intramolecular van der Waals energy suggests that the rupture of the tight packing during the initial unfolding phase contributes to the energy barrier of the denaturation process. The mutationally well-analyzed Asp8-Arg110-Asp12 double salt-bridge on the barnase surface is found to be marginally stable in the folded form in the simulations. A Poisson-Boltzmann calculation indicates that

  11. Stratification in Drying Polymer-Polymer and Colloid-Polymer Mixtures. (United States)

    Howard, Michael P; Nikoubashman, Arash; Panagiotopoulos, Athanassios Z


    Drying polymer-polymer and colloid-polymer mixtures were studied using Langevin dynamics computer simulations. Polymer-polymer mixtures vertically stratified into layers, with the shorter polymers enriched near the drying interface and the longer polymers pushed down toward the substrate. Colloid-polymer mixtures stratified into a polymer-on-top structure when the polymer radius of gyration was comparable to or smaller than the colloid diameter, and a colloid-on-top structure otherwise. We also developed a theoretical model for the drying mixtures based on dynamical density functional theory, which gave excellent quantitative agreement with the simulations for the polymer-polymer mixtures and qualitatively predicted the observed polymer-on-top or colloid-on-top structures for the colloid-polymer mixtures.

  12. Multidimensional differential display via ion-pair reversed-phase denaturing high-performance liquid chromatography. (United States)

    Matin, Maryam M; Andrews, Peter W; Hornby, David P


    Experimental approaches are now available for the analysis of whole transcriptome expression in cells and tissues. Since the introduction of such methods for the investigation of differences in mRNA populations, they have been applied successfully to many areas of biology and medicine including development, differentiation, physiology, pharmacology, and carcinogenesis. Here we describe an improved and automated approach based on the differential mRNA display method developed by Liang and Pardee (P. Liang and A. B. Pardee, 1992, Science 257, 967-971). We report the use of ion-pair reversed-phase denaturing high-performance liquid chromatography (IP RP DHPLC), for the first time, to produce a "fingerprint," after amplification of the cDNA corresponding to the mRNA populations, from two or more of the samples that are to be compared. By overlaying the chromatograms produced from the amplification of different samples derived from the same set of oligodeoxynucleotide primers, those genes that are differentially expressed can be selected and subsequently cloned and sequenced rapidly to establish a profile of differentially expressed genes. In addition, validation of the data obtained is readily achieved by this method using IP RP DHPLC and quantitative RT-PCR. In this study total RNA was prepared from NTERA2 cells before and after differentiation induced by retinoic acid and was reverse-transcribed into cDNA prior to amplification to produce fluorescently tagged products. This methodology facilitates multiple rounds of interrogation of RT-PCR products and we tentatively refer to this approach as Multidimensional Differential Display. (c)2002 Elsevier Science (USA).

  13. Allosteric effectors and trehalose protect larval Manduca sexta fat body glycogen phosphorylase B against thermal denaturation. (United States)

    Meyer-Fernandes, J R; Arrese, E L; Wells, M A


    In this paper we assessed the ability of modulators of the activity of glycogen phosphorylase b from the fat body of larval Manduca sexta to stabilize the enzyme against thermal denaturation. This approach has allowed us to distinguish between modulators that stabilize the enzyme, presumably through some conformational effect, from those that do not affect thermal stability. For example, 5'-AMP and 5'-IMP are both positive modulators of the enzyme and the K(m)s for AMP and IMP were similar, 0.71 and 1.09 mM, respectively. However, the V(max) for AMP (123 nmol/mg/min) was 10 times higher than the value found for IMP (12.5 nmol/mg/min) and AMP increased the thermal stability of glycogen phosphorylase b, however IMP did not increase the enzyme's thermal stability. Indeed, IMP decreased both the allosteric activation of the enzyme by AMP and the thermal protection conferred by AMP. The allosteric inhibitors ADP and ATP, which in vertebrate phosphorylase bind to the same site as AMP, both increased the thermal stability of the enzyme, however with less efficiency than AMP. Inorganic phosphate increased thermal stability, but glycogen and amylose did not. Glycerol, at 600 mM, protected the enzyme against thermal inactivation, whereas sorbitol at the same concentration did not show any effect. Among the polyols tested, trehalose was the most effective in conferring thermal stability. In fact, in the presence of 20 mM AMP and 600 mM trehalose, 90% of the enzyme activity remained after 20 min at 60 degrees C.

  14. An improved method for detecting genetic variation in DNA using denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    Takahashi, Norio; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.


    We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that use of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than use of DNA:DNA heteroduplexes, because preparation of RNA probes is easier than that of DNA probes. Three different 32 P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of a mismatch(es) was detected as a difference in the mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and three thalassemic human β-globin genes. The results from experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human β-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was undertaken in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for detecting heritable variation and should be a powerful tool for detecting fresh mutations in DNA, which occur outside the known restriction sites. (author)

  15. Star-Branched Polymers (Star Polymers)

    KAUST Repository

    Hirao, Akira


    The synthesis of well-defined regular and asymmetric mixed arm (hereinafter miktoarm) star-branched polymers by the living anionic polymerization is reviewed in this chapter. In particular, much attention is being devoted to the synthetic development of miktoarm star polymers since 2000. At the present time, the almost all types of multiarmed and multicomponent miktoarm star polymers have become feasible by using recently developed iterative strategy. For example, the following well-defined stars have been successfully synthesized: 3-arm ABC, 4-arm ABCD, 5-arm ABCDE, 6-arm ABCDEF, 7-arm ABCDEFG, 6-arm ABC, 9-arm ABC, 12-arm ABC, 13-arm ABCD, 9-arm AB, 17-arm AB, 33-arm AB, 7-arm ABC, 15-arm ABCD, and 31-arm ABCDE miktoarm star polymers, most of which are quite new and difficult to synthesize by the end of the 1990s. Several new specialty functional star polymers composed of vinyl polymer segments and rigid rodlike poly(acetylene) arms, helical polypeptide, or helical poly(hexyl isocyanate) arms are introduced.

  16. A novel ionic liquid monolithic column and its separation properties in capillary electrochromatography. (United States)

    Wang, Yu; Deng, Qi-Liang; Fang, Guo-Zhen; Pan, Ming-Fei; Yu, Yang; Wang, Shuo


    A novel ionic liquid (IL) monolithic capillary column was successfully prepared by thermal free radical copolymerization of IL (1-vinyl-3-octylimidazolium chloride, ViOcIm(+)Cl(-)) together with lauryl methacrylate (LMA) as the binary functional monomers and ethylene dimethacrylate (EDMA) as the cross-linker in binary porogen. The proportion of monomers, porogens and cross-linker in the polymerization mixture was optimized in detail. The resulting IL-monolithic column could not only generate a stable reversed electroosmotic flow (EOF) in a wide pH range (2.0-12.0), but also effectively eliminate the wall adsorption of the basic analytes. The obtained IL-monolithic columns were examined by scanning electron microscopy (SEM) and Fourier transform infrared (FT-IR). These results indicated that the IL-monolithic capillary column possessed good pore properties, mechanical stability and permeability. The column performance was also evaluated by separating different kinds of compounds, such as alkylbenzenes, thiourea and its analogues, and amino acids. The lowest plate height of ~6.8 μm was obtained, which corresponded to column efficiency (theoretical plates, N) of ~147,000 plates m(-1) for thiourea. ILs, as a new type of functional monomer, present a promising option in the fabrication of the organic polymer-based monolithic columns in CEC. Copyright © 2011 Elsevier B.V. All rights reserved.

  17. Raman spectral markers of collagen denaturation and hydration in human cortical bone tissue are affected by radiation sterilization and high cycle fatigue damage. (United States)

    Flanagan, Christopher D; Unal, Mustafa; Akkus, Ozan; Rimnac, Clare M


    Thermal denaturation and monotonic mechanical damage alter the organic and water-related compartments of cortical bone. These changes can be detected using Raman spectroscopy. However, less is known regarding Raman sensitivity to detect the effects of cyclic fatigue damage and allograft sterilization doses of gamma radiation. To determine if Raman spectroscopic biomarkers of collagen denaturation and hydration are sensitive to the effects of (a) high cycle fatigue damage and (b) 25kGy irradiation. Unirradiated and gamma-radiation sterilized human cortical bone specimens previously tested in vitro under high-cycle (> 100,000 cycles) fatigue conditions at 15MPa, 25MPa, 35MPa, 45MPa, and 55MPa cyclic stress levels were studied. Cortical bone Raman spectral profiles from wavenumber ranges of 800-1750cm -1 and 2700-3800cm -1 were obtained and compared from: a) non-fatigue vs fatigue fracture sites and b) radiated vs. unirradiated states. Raman biomarker ratios 1670/1640 and 3220/2949, which reflect collagen denaturation and organic matrix (mainly collagen)-bound water, respectively, were assessed. One- and two-way ANOVA analyses were utilized to identify differences between groups along with interaction effects between cyclic fatigue and radiation-induced damage. Cyclic fatigue damage resulted in increases in collagen denaturation (1670/1640: 1.517 ± 0.043 vs 1.579 ± 0.021, p collagen denaturation (r = 0.514, p collagen)-bound water. A Raman measure of collagen denaturation was sensitive to cyclic fatigue damage but not 25kGy irradiation. Collagen denaturation was correlated with organic matrix-bound water, suggesting that denaturation of collagen to gelatinous form may expose more binding sites to water by unwinding the triple alpha chains. This research may eventually be useful to help identify allograft quality and more appropriately match donors to recipients. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Artificially Engineered Protein Polymers. (United States)

    Yang, Yun Jung; Holmberg, Angela L; Olsen, Bradley D


    Modern polymer science increasingly requires precise control over macromolecular structure and properties for engineering advanced materials and biomedical systems. The application of biological processes to design and synthesize artificial protein polymers offers a means for furthering macromolecular tunability, enabling polymers with dispersities of ∼1.0 and monomer-level sequence control. Taking inspiration from materials evolved in nature, scientists have created modular building blocks with simplified monomer sequences that replicate the function of natural systems. The corresponding protein engineering toolbox has enabled the systematic development of complex functional polymeric materials across areas as diverse as adhesives, responsive polymers, and medical materials. This review discusses the natural proteins that have inspired the development of key building blocks for protein polymer engineering and the function of these elements in material design. The prospects and progress for scalable commercialization of protein polymers are reviewed, discussing both technology needs and opportunities.

  19. Radiation energy transfer in RNA polymers (United States)

    Kempner, E. S.; Salovey, R.; Bernstein, S. L.


    Ribozymes are a special class of polyribonucleotide (RNA) molecules which possess intrinsic catalytic activity, capable of cleaving nucleic acid substrates. RNA molecules were synthesized containing a hammerhead ribozyme moiety of 52 nucleotides linked to an inactive leader sequence, for total lengths of either 262 or 1226 nucleotides. These RNAs were frozen and irradiated with high energy electrons. Surviving ribozyme activity was determined, using the ability of the irradiated ribozymes to cleave a labeled substrate. From the same irradiated samples, the amount of intact RNA remaining was determined following denaturing gel electrophoresis. Radiation target analyses of these data revealed a structural target size of 80 kDa and a ribozyme activity target size of 15 kDa for the smaller ribozyme, and 319 and 16 kDa, respectively, for the larger ribozyme. The disparity in target size for activity vs structure indicates that, in contrast to proteins, there is no spread of radiation damage far from the primary site of ionization in RNA molecules. The smaller target size for activity indicates that only primary ionizations occurring in the specific active region are effective. This is similar to the case for oligosaccharides. It is concluded that the presence of the ribose sugar in the polymer chain restricts radiation damage to a small region and prevents major energy transfer throughout the molecule.

  20. Internally plasticised cellulose polymers

    International Nuclear Information System (INIS)

    Burnup, M.; Hayes, G.F.; Fydelor, P.J.


    Plasticised cellulose polymers comprise base polymer having a chain of β-anhydroglucose units joined by ether linkages, with at least one of said units carrying at least one chemically unreactive side chain derived from an allylic monomer or a vinyl substituted derivative of ferrocene. The side chains are normally formed by radiation grafting. These internally plasticised celluloses are useful in particular as inhibitor coatings for rocket motor propellants and in general wherever cellulose polymers are employed. (author)

  1. Characterisation of polymers, 1

    CERN Document Server

    Crompton, Roy


    This essential guide to Polymer Characterisation is a complete compendium of methodologies that have evolved for the determination of the chemical composition of polymers. This 478-page book gives an up-to-date and thorough exposition of the state-of-the-art theories and availability of instrumentation needed to effect chemical and physical analysis of polymers. This is supported by approximately 1200 references. Volume 1 covers the methodology used for the determination of metals, non-metals and organic functional groups in polymers, and for the determination of the ratio in which different m

  2. Smartphone Cortex Controlled Real-Time Image Processing and Reprocessing for Concentration Independent LED Induced Fluorescence Detection in Capillary Electrophoresis. (United States)

    Szarka, Mate; Guttman, Andras


    We present the application of a smartphone anatomy based technology in the field of liquid phase bioseparations, particularly in capillary electrophoresis. A simple capillary electrophoresis system was built with LED induced fluorescence detection and a credit card sized minicomputer to prove the concept of real time fluorescent imaging (zone adjustable time-lapse fluorescence image processor) and separation controller. The system was evaluated by analyzing under- and overloaded aminopyrenetrisulfonate (APTS)-labeled oligosaccharide samples. The open source software based image processing tool allowed undistorted signal modulation (reprocessing) if the signal was inappropriate for the actual detection system settings (too low or too high). The novel smart detection tool for fluorescently labeled biomolecules greatly expands dynamic range and enables retrospective correction for injections with unsuitable signal levels without the necessity to repeat the analysis.

  3. A novel ionic liquid monolithic column and its separation properties in capillary electrochromatography

    International Nuclear Information System (INIS)

    Wang Yu; Deng Qiliang; Fang Guozhen; Pan Mingfei; Yu Yang; Wang Shuo


    Highlights: ► ILs as functional monomer for capillary monolithic column. ► Separation of alkylbenzenes, thiourea analogues, and amino acids. ► The column generate a stable reversed EOF from pH 2.0 to 12.0. ► The column efficiency of 147,000 plates m −1 was obtained for thiourea. - Abstract: A novel ionic liquid (IL) monolithic capillary column was successfully prepared by thermal free radical copolymerization of IL (1-vinyl-3-octylimidazolium chloride, ViOcIm + Cl − ) together with lauryl methacrylate (LMA) as the binary functional monomers and ethylene dimethacrylate (EDMA) as the cross-linker in binary porogen. The proportion of monomers, porogens and cross-linker in the polymerization mixture was optimized in detail. The resulting IL-monolithic column could not only generate a stable reversed electroosmotic flow (EOF) in a wide pH range (2.0–12.0), but also effectively eliminate the wall adsorption of the basic analytes. The obtained IL-monolithic columns were examined by scanning electron microscopy (SEM) and Fourier transform infrared (FT-IR). These results indicated that the IL-monolithic capillary column possessed good pore properties, mechanical stability and permeability. The column performance was also evaluated by separating different kinds of compounds, such as alkylbenzenes, thiourea and its analogues, and amino acids. The lowest plate height of ∼6.8 μm was obtained, which corresponded to column efficiency (theoretical plates, N) of ∼147,000 plates m −1 for thiourea. ILs, as a new type of functional monomer, present a promising option in the fabrication of the organic polymer-based monolithic columns in CEC.

  4. Binary Polymer Brushes of Strongly Immiscible Polymers. (United States)

    Chu, Elza; Babar, Tashnia; Bruist, Michael F; Sidorenko, Alexander


    The phenomenon of microphase separation is an example of self-assembly in soft matter and has been observed in block copolymers (BCPs) and similar materials (i.e., supramolecular assemblies (SMAs) and homo/block copolymer blends (HBCs)). In this study, we use microphase separation to construct responsive polymer brushes that collapse to generate periodic surfaces. This is achieved by a chemical reaction between the minor block (10%, poly(4-vinylpyridine)) of the block copolymer and a substrate. The major block of polystyrene (PS) forms mosaic-like arrays of grafted patches that are 10-20 nm in size. Depending on the nature of the assembly (SMA, HBC, or neat BCP) and annealing method (exposure to vapors of different solvents or heating above the glass transition temperature), a range of "mosaic" brushes with different parameters can be obtained. Successive grafting of a secondary polymer (polyacrylamide, PAAm) results in the fabrication of binary polymer brushes (BPBs). Upon being exposed to specific selective solvents, BPBs may adopt different conformations. The surface tension and adhesion of the binary brush are governed by the polymer occupying the top stratum. The "mosaic" brush approach allows for a combination of strongly immiscible polymers in one brush. This facilitates substantial contrast in the surface properties upon switching, previously only possible for substrates composed of predetermined nanostructures. We also demonstrate a possible application of such PS/PAAm brushes in a tunable bioadhesion-bioadhesive (PS on top) or nonbioadhesive (PAAm on top) surface as revealed by Escherichia coli bacterial seeding.

  5. Investigating the fermentation of cocoa by correlating denaturing gradient gel electrophoresis profiles and near infrared spectra. (United States)

    Nielsen, Dennis S; Snitkjaer, Pia; van den Berg, Frans


    Raw cocoa has an astringent, unpleasant taste and flavour, and has to be fermented, dried and roasted in order to obtain the characteristic cocoa flavour and taste. During the fermentation microbial activity outside the cocoa beans induces biochemical and physical changes inside the beans. The process is complex involving activity of several different groups of microorganisms which bring about numerous biochemical and physical changes inside the beans. Due to the complexity of these processes no thorough investigations of the interactions between the microbial activities on the outside of the beans and the chemical processes inside the beans have been carried out previously. Recently it has been shown that Denaturing Gradient Gel Electrophoresis (DGGE) offers an efficient tool for monitoring the microbiological changes taking place during the fermentation of cocoa. Near Infrared (NIR) spectroscopy has previously been used to determine various components in cocoa beans, offering a rapid alternative compared to traditional analytical methods for obtaining knowledge about changes in the chemical composition of the cocoa beans during fermentation. During a number of cocoa fermentations bean samples were taken with 24 h intervals to be dried and analysed by NIR. Cocoa pulp samples taken simultaneously during the same fermentations have previously been characterised using DGGE [Nielsen, D.S., Teniola, O.D., Ban-Koffi, L., Owusu, M., Andersson, T., Holzapfel, W.H. (2007). The microbiology of Ghanaian cocoa fermentations analysed using culture dependent and culture-independent methods. International Journal of Food Microbiology 114, 168-186.]. Here we report the first study where microbiological changes during the fermentation determined using DGGE are correlated to changes inside the beans determined by NIR using multivariate data analysis. Following data pre-processing (baseline correction followed by Co-shift correction or Correlation Optimised Warping) the DGGE spectra

  6. Influence of the sample volume and the position of the electrode and the capillary-end in the sample vial on the electrokinetic injection in capillary electrophoresis

    NARCIS (Netherlands)

    Ensing, K


    The influence of the positions of the electrode and the capillary-end and volume in the sample vials on the electrokinetically injected amount of the analytes in capillary electrophoresis was studied. The influence may be reduced by using a more or less fixed position of the electrode and the

  7. Polymers targeting habitual diseases (United States)

    The use of polymeric drug conjugates mainly for the treatment for cancer therapy has been addressed, but these polymers also find their way in treatment of various lifestyle disorders like diabetes, hypertension, cardiovascular diseases etc. The focus is being laid to develop biodegradable polymer ...

  8. Stiff Quantum Polymers


    Kleinert, H.


    At ultralow temperatures, polymers exhibit quantum behavior, which is calculated here for the second and fourth moments of the end-to-end distribution in the large-stiffness regime. The result should be measurable for polymers in wide optical traps.

  9. Segmented conjugated polymers

    Indian Academy of Sciences (India)

    Segmented conjugated polymers, wherein the conjugation is randomly truncated by varying lengths of non-conjugated segments, form an interesting class of polymers as they not only represent systems of varying stiffness, but also ones where the backbone can be construed as being made up of chromophores of varying ...

  10. Elastic lattice polymers

    NARCIS (Netherlands)

    Baiesi, M.; Barkema, G.T.; Carlon, E.


    We study a model of “elastic” lattice polymer in which a fixed number of monomers m is hosted by a self-avoiding walk with fluctuating length l. We show that the stored length density m 1− l /m scales asymptotically for large m as m= 1− /m+. . . , where is the polymer entropic exponent, so that can

  11. Polymer gels and networks

    National Research Council Canada - National Science Library

    Osada, Yoshihito; Khokhlov, A. R


    ... or magnetic field, etc.). It was realized that not only can polymer gels absorb and hold a considerable volume of liquids, but they can also be forced to expel the absorbed liquid in a controlled manner. Of particular interest are hydrogels, i.e., polymer gels, which swell extensively in water. The most common hydrogels are polyelectrolyte gels: ...

  12. Polymer light emitting diodes

    International Nuclear Information System (INIS)

    Gautier-Thianche, Emmmanuelle


    We study sandwich type semiconducting polymer light emitting diodes; anode/polymer/cathode. ITO is selected as anode, this polymer is a blend of a commercially available polymer with a high hole transport ability: polyvinyl-carbazole and a laser dye: coumarin-515. Magnesium covered with silver is chosen for the anode. We study the influence of polymer thickness and coumarin doping ratio on electroluminescence spectrum, electric characteristics and quantum efficiency. An important drawback is that diodes lifetime remains low. In the second part of our study we determine degradations causes with X-Ray reflectivity experiments. It may be due to ITO very high roughness. We realize a new type of planar electroluminescent device: a channel type electroluminescent device in which polymer layer is inserted into an aluminium channel. Such a device is by far more stable than using classical sandwich structures with the same polymer composition: indeed, charges are generated by internal-field ionization and there is no injection from the electrode to the polymer. This avoids electrochemical reactions at electrodes, thus reducing degradations routes. (author) [fr

  13. Polymers for Combating Biocorrosion

    Directory of Open Access Journals (Sweden)

    Jing Guo


    Full Text Available Biocorrosion has been considered as big trouble in many industries and marine environments due to causing of great economic loss. The main disadvantages of present approaches to prevent corrosion include being limited by environmental factors, being expensive, inapplicable to field, and sometimes inefficient. Studies show that polymer coatings with anticorrosion and antimicrobial properties have been widely accepted as a novel and effective approach to prevent biocorrosion. The main purpose of this review is to summarize up the progressive status of polymer coatings used for combating microbial corrosion. Polymers used to synthesize protective coatings are generally divided into three categories: (i traditional polymers incorporated with biocides, (ii antibacterial polymers containing quaternary ammonium compounds, and (iii conductive polymers. The strategies to synthesize polymer coatings resort mainly to grafting antibacterial polymers from the metal substrate surface using novel surface-functionalization approaches, such as free radical polymerization, chemically oxidative polymerization, and surface-initiated atom transfer radical polymerization, as opposed to the traditional approaches of dip coating or spin coating.

  14. Ion Implantation of Polymers

    DEFF Research Database (Denmark)

    Popok, Vladimir


    is put on the low-energy implantation of metal ions causing the nucleation and growth of nanoparticles in the shallow polymer layers. Electrical, optical and magnetic properties of metal/polymer composites are under the discussion and the approaches towards practical applications are overviewed....

  15. Conducting polymer hydrogels

    Czech Academy of Sciences Publication Activity Database

    Stejskal, Jaroslav


    Roč. 71, č. 2 (2017), s. 269-291 ISSN 0366-6352 R&D Projects: GA ČR(CZ) GA16-02787S Institutional support: RVO:61389013 Keywords : aerogel * conducting polymers * conductivity Subject RIV: CD - Macromolecular Chemistry OBOR OECD: Polymer science Impact factor: 1.258, year: 2016

  16. based gel polymer electrolytes

    Indian Academy of Sciences (India)

    operating systems. With this situation, attempts have been made in poly (ethylene oxide) (PEO) based polymer electrolytes to reach an appreciable electrical conducti- vity at ambient temperature (Wright 1975; Martuscelli et al 1984). Generally solid polymer electrolytes have many advantages, viz. high ionic conductivity, ...

  17. PEO polymer electrolytes

    Indian Academy of Sciences (India)


    vs temperature plots showed the enhancement of conductivity with TiO2 added nanocomposite ceramic fillers. The enhanced conductivity is ... developing mixed polymer electrolyte by using a novel class of plasticizers. Classical polymer ..... phology of the ceramic filler could optimize the conduc- tion. This might lead to the ...

  18. Doped Chiral Polymer Metamaterials Project (United States)

    National Aeronautics and Space Administration — Doped Chiral Polymer Metamaterials (DCPM) with tunable resonance frequencies have been developed by adding plasmonic inclusions into chiral polymers with variable...


    Directory of Open Access Journals (Sweden)

    Mudasir Mudasir


    Full Text Available A research about base-pair specificity of the DNA binding of [Fe(phen3]2+, [Fe(phen2(dip]2+ and [Fe(phen(dip2]2+ complexes and the effect of calf-thymus DNA (ct-DNA binding of these metal complexes on thermal denaturation of ct-DNA has been carried out. This research is intended to evaluate the preferential binding of the complexes to the sequence of DNA (A-T or G-C sequence and to investigate the binding strength and mode upon their interaction with DNA. Base-pair specificity of the DNA binding of the complexes was determined by comparing the equilibrium binding constant (Kb of each complex to polysynthetic DNA that contain only A-T or G-C sequence. The Kb value of the interaction was determined by spectrophotometric titration and thermal denaturation temperature (Tm was determined by monitoring the absorbance of the mixture solution of each complex and ct-DNA at λ =260 nm as temperature was elevated in the range of 25 - 100 oC. Results of the study show that in general all iron(II complexes studied exhibit a base-pair specificity in their DNA binding to prefer the relatively facile A-T sequence as compared to the G-C one. The thermal denaturation experiments have demonstrated that Fe(phen3]2+ and [Fe(phen2(dip]2+ interact weakly with double helical DNA via electrostatic interaction as indicated by insignificant changes in melting temperature, whereas [Fe(phen2(dip]2+  most probably binds to DNA in mixed modes of interaction, i.e.: intercalation and electrostatic interaction. This conclusion is based on the fact that the binding of [Fe(phen2(dip]2+ to ct-DNA moderately increase the Tm value of ct- DNA   Keywords: DNA Binding, mixed-ligand complexes

  20. Denatured states of yeast cytochrome c induced by heat and guanidinium chloride are structurally and thermodynamically different. (United States)

    Zaidi, Sobia; Haque, Md Anzarul; Ubaid-Ullah, Shah; Prakash, Amresh; Hassan, Md Imtaiyaz; Islam, Asimul; Batra, Janendra K; Ahmad, Faizan


    A sequence alignment of mammalian cytochromes c with yeast iso-1-cytochrome c (y-cyt-c) shows that the yeast protein contains five extra N-terminal residues. We have been interested in understanding the question: What is the role of these five extra N-terminal residues in folding and stability of the protein? To answer this question we have prepared five deletants of y-cyt-c by sequentially removing these extra residues. During our studies on the wild type (WT) protein and its deletants, we observed that the amount of secondary structure in the guanidinium chloride (GdmCl)-induced denatured (D) state of each protein is different from that of the heat-induced denatured (H) state. This finding is confirmed by the observation of an additional cooperative transition curve of optical properties between H and D states on the addition of different concentrations of GdmCl to the already heat denatured WT y-cyt-c and its deletants at pH 6.0 and 68°C. For each protein, analysis of transition curves representing processes, native (N) state ↔ D state, N state ↔ H state, and H state ↔ D state, was done to obtain Gibbs free energy changes associated with all the three processes. This analysis showed that, for each protein, thermodynamic cycle accommodates Gibbs free energies associated with transitions between N and D states, N and H states, and H and D states, the characteristics required for a thermodynamic function. All these experimental observations have been supported by our molecular dynamics simulation studies.

  1. All Polymer Micropump

    DEFF Research Database (Denmark)

    Hansen, Thomas Steen


    In this thesis an all polymer micropump, and the fabrication method required to fabricate this, are examined. Polymer microfluidic. devices are of major scientific interest because they can combine complicated chemical and biological analys~s in cheap and disposable devices. The electrode system...... in the micropump is based on the conducting polymer poly(3,4 ethylenedioxythiophene) (PEDOT). The majority of the work conducted was therefore aimed at developing methods for patterning and processing PEDOT. First a method was developed, where the conducting polymer PEDOT can be integrated into non...... of the substrate, the PEDOT is integrated into the non-conductive polymer. The result is a material that retains the good conductivity of PEDOT, but gains the mechanical stability of the substrate. The best results were obtained for PEDOTjPMMA. The new mechanically stable PEDOTjPMMA was micro-patterned using clean...

  2. Polymer wear evaluation

    DEFF Research Database (Denmark)

    Lagerbon, Mikkel; Sivebæk, Ion Marius


    Polymer wear plays an increasing role in manufacturing of machine parts for e.g. medical devices. Some of these have an expected lifetime of five to eight years during which very little wear of the components is acceptable. Too much wear compromises the dosage accuracy of the device and thereby...... the safety of the patients. Prediction of the wear of polymers is complicated by the low thermal conductivity of this kind of material. It implies that any acceleration of testing conditions by increased contact pressure and/or sliding velocity will make the polymer fail due to exaggerated heat buildup....... This is not the kind of wear observed in medical devices. In the present work a method was developed capable of evaluating the wear progression in polymer-polymer contacts. The configuration of the setup is injection moulded specimens consisting of an upper part having a toroid shape and a lower flat part. The sliding...

  3. Mutation analysis in {beta}{sub 2-}adrenergic receptor gene by denaturing high performance liquid chromatography (DHPLC)

    Energy Technology Data Exchange (ETDEWEB)

    Park, S.B.; Oh, C.H.; Kim, J.W.; Jang, W.C. [Dankook University, Cheonan (Korea)


    We analysed mutation of {beta}{sub 2-}adrenergic receptor gene that controls bronchial asthma by denaturing high performance liquid chromatography (DHPLC) according to ion-pair reversed-phase high performance liquid chromatography (IP-RP-HPLC). We extracted genomic DNA from 50 asthma patients, amplified DNA using PCR, and analysed PCR product by DHPLC. As a result, we obtained that mutation frequency was 15(30%) among 50 cases. Consequently DHPLC mutation detection was confirmed that the result of direct sequencing was coincide exactly. (author). 13 refs., 4 figs.

  4. Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA

    Directory of Open Access Journals (Sweden)

    Metsis Madis


    Full Text Available Abstract Background In a traditional electrophoresis mobility shift assay (EMSA a 32P-labeled double-stranded DNA oligonucleotide or a restriction fragment bound to a protein is separated from the unbound DNA by polyacrylamide gel electrophoresis (PAGE in nondenaturing conditions. An extension of this method uses the large population of fragments derived from long genomic regions (approximately 600 kb for the identification of fragments containing protein binding regions. With this method, genomic DNA is fragmented by restriction enzymes, fragments are amplified by PCR, radiolabeled, incubated with nuclear proteins and the resulting DNA-protein complexes are separated by two-dimensional PAGE. Shifted DNA fragments containing protein binding sites are identified by using additional procedures, i. e. gel elution, PCR amplification, cloning and sequencing. Although the method allows simultaneous analysis of a large population of fragments, it is relatively laborious and can be used to detect only high affinity protein binding sites. Here we propose an alternative and straightforward strategy which is based on a combination of native and denaturing PAGE. This strategy allows the identification of DNA fragments containing low as well as high affinity protein binding regions, derived from genomic DNA ( Results We have combined an EMSA-based selection step with subsequent denaturing PAGE for the localization of protein binding regions in long (up to10 kb fragments of genomic DNA. Our strategy consists of the following steps: digestion of genomic DNA with a 4-cutter restriction enzyme (AluI, BsuRI, TruI, etc, separation of low and high molecular weight fractions of resultant DNA fragments, 32P-labeling with Klenow polymerase, traditional EMSA, gel elution and identification of the shifted bands (or smear by denaturing PAGE. The identification of DNA fragments containing protein binding sites is carried out by running the gel-eluted fragments alongside

  5. Heterogeneity of equilibrium molten globule state of cytochrome c induced by weak salt denaturants under physiological condition.

    Directory of Open Access Journals (Sweden)

    Hamidur Rahaman

    Full Text Available While many proteins are recognized to undergo folding via intermediate(s, the heterogeneity of equilibrium folding intermediate(s along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD, ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS were used to study the structural and thermodynamic characteristics of the native (N, denatured (D and intermediate state (X of goat cytochorme c (cyt-c induced by weak salt denaturants (LiBr, LiCl and LiClO4 at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε400 and CD ([θ]409, is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO4 and acidic pH. Our observations suggest: (1 that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III axial bond and Trp59-propionate interactions; (2 that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO4 and 0.5 M NaCl at pH 2.0; and (3 that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1, classical (X2 and disordered (X3, i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N.

  6. Thermal-Induced Denaturation and Aggregation Behavior of Lysozyme and Bovine Serum Albumin: a Thermodynamic and Structural Study (United States)

    Perez, Aline Sanches; Oliveira, Cristiano Luis Pinto


    Solution studies permit a direct investigation of the particles on a well-defined environment. Fluorescence, circular dichroism, scattering, and calorimetry provide, individually, very important information among the protein structure, overall shape, and thermodynamic equilibrium. In this work, a combination of these techniques is presented for the study of denaturation induced by temperature of two well-known proteins, Henn Egg lysozyme and bovine serum albumin. A detailed thermodynamic and structural investigation is shown for these proteins, providing interesting information on the thermal-induced changes in the protein structure and aggregation behavior.

  7. Pressure-assisted cold denaturation of hen egg white lysozyme: the influence of co-solvents probed by hydrogen exchange nuclear magnetic resonance

    Directory of Open Access Journals (Sweden)

    Vogtt K.


    Full Text Available COSY proton nuclear magnetic resonance was used to measure the exchange rates of amide protons of hen egg white lysozyme (HEWL in the pressure-assisted cold-denatured state and in the heat-denatured state. After dissolving lysozyme in deuterium oxide buffer, labile protons exchange for deuterons in such a way that exposed protons are substituted rapidly, whereas "protected" protons within structured parts of the protein are substituted slowly. The exchange rates k obs were determined for HEWL under heat treatment (80ºC and under high pressure conditions at low temperature (3.75 kbar, -13ºC. Moreover, the influence of co-solvents (sorbitol, urea on the exchange rate was examined under pressure-assisted cold denaturation conditions, and the corresponding protection factors, P, were determined. The exchange kinetics upon heat treatment was found to be a two-step process with initial slow exchange followed by a fast one, showing residual protection in the slow-exchange state and P-factors in the random-coil-like range for the final temperature-denatured state. Addition of sorbitol (500 mM led to an increase of P-factors for the pressure-assisted cold denatured state, but not for the heat-denatured state. The presence of 2 M urea resulted in a drastic decrease of the P-factors of the pressure-assisted cold denatured state. For both types of co-solvents, the effect they exert appears to be cooperative, i.e., no particular regions within the protein can be identified with significantly diverse changes of P-factors.

  8. Polymer-Polymer Miscibility and Enthalpy Relaxations

    NARCIS (Netherlands)

    Bosma, Martin; Brinke, Gerrit ten; Ellis, Thomas S.

    Annealing of polymers below the glass transition temperature results in a decrease in enthalpy that is recovered during heating. The enthalpy recovery is visible as an endothermic peak in a differential scanning calorimetry (DSC) scan. The position of this peak depends on the thermal treatment given

  9. Photoluminescence in conjugated polymers

    International Nuclear Information System (INIS)

    Furst, J.E.; Laugesen, R.; Dastoor, P.; McNeill, C.


    Full text: Conjugated polymers combine the electronic and optical properties of semiconductors with the processability of polymers. They contain a sequence of alternate single and double carbon bonds so that the overlap of unhybridised p z orbitals creates a delocalised ρ system which gives semiconducting properties with p-bonding (valence) and p* -antibonding (conduction) bands. Photoluminesence (PL) in conjugated polymers results from the radiative decay of singlet excitons confined to a single chain. The present work is the first in a series of studies in our laboratory that will characterize the optical properties of conjugated polymers. The experiment involves the illumination of thin films of conjugated polymer with UV light (I=360 nm) and observing the subsequent fluorescence using a custom-built, fluorescence spectrometer. Photoluminesence spectra provide basic information about the structure of the polymer film. A typical spectrum is shown in the accompanying figure. The position of the first peak is related to the polymer chain length and resolved multiple vibronic peaks are an indication of film structure and morphology. We will also present results related to the optical degradation of these materials when exposed to air and UV light

  10. Purification of inclusion bodies using PEG precipitation under denaturing conditions to produce recombinant therapeutic proteins from Escherichia coli. (United States)

    Chen, Huanhuan; Li, Ninghuan; Xie, Yueqing; Jiang, Hua; Yang, Xiaoyi; Cagliero, Cedric; Shi, Siwei; Zhu, Chencen; Luo, Han; Chen, Junsheng; Zhang, Lei; Zhao, Menglin; Feng, Lei; Lu, Huili; Zhu, Jianwei


    It has been documented that the purification of inclusion bodies from Escherichia coli by size exclusion chromatography (SEC) may benefit subsequent refolding and recovery of recombinant proteins. However, loading volume and the high cost of the column limits its application in large-scale manufacturing of biopharmaceutical proteins. We report a novel process using polyethylene glycol (PEG) precipitation under denaturing conditions to replace SEC for rapid purification of inclusion bodies containing recombinant therapeutic proteins. Using recombinant human interleukin 15 (rhIL-15) as an example, inclusion bodies of rhIL-15 were solubilized in 7 M guanidine hydrochloride, and rhIL-15 was precipitated by the addition of PEG 6000. A final concentration of 5% (w/v) PEG 6000 was found to be optimal to precipitate target proteins and enhance recovery and purity. Compared to the previously reported S-200 size exclusion purification method, PEG precipitation was easier to scale up and achieved the same protein yields and quality of the product. PEG precipitation also reduced manufacturing time by about 50 and 95% of material costs. After refolding and further purification, the rhIL-15 product was highly pure and demonstrated a comparable bioactivity with a rhIL-15 reference standard. Our studies demonstrated that PEG precipitation of inclusion bodies under denaturing conditions holds significant potential as a manufacturing process for biopharmaceuticals from E. coli protein expression systems.

  11. Evidence of β-sheet structure induced kinetic stability of papain upon thermal and sodium dodecyl sulphate denaturation

    Directory of Open Access Journals (Sweden)

    Rašković Brankica


    Full Text Available Papain is a protease that consists of α-helical and β-sheet domains which unfold almost independently. Both, papain considerable thermal stability and sodium dodecyl sulphate (SDS resistance have been shown. However, the ability of each domain to unfold upon thermal and SDS denaturation has never been studied. This work shows that fruit papain has slightly higher thermal inactivation resistance when it is compared to stem papain with rather high activation energy (Ea of 223 ± 16 kJmol-1 and Tm50 value of 79 ± 2 °C. SDS resistance of fruit papain was estimated by SDS-PAGE analysis and activity staining. It has been noted that, in the presence of SDS, unless heat energy was applied in order to unfold papain, the protein remained active. Furthermore, it has been proven via Fourier transform infrared spectroscopy (FT-IR that α-helical domain of fruit papain is more prone to unfolding at elevated temperatures and in the presence of SDS then β-sheet rich domain. Thermal denaturation of papain without detergent present led to accelerated formation of aggregation specific intermolecular β-sheets as compared to native protein. Presented results are both, of fundamental and application importance. [Projekat Ministarstva nauke Republike Srbije, br. 172049

  12. Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides

    International Nuclear Information System (INIS)

    Oh, Kwang-Im; Jung, Young-Sang; Hwang, Geum-Sook; Cho, Minhaeng


    Understanding intrinsic conformational preferences of amino-acids in unfolded proteins is important for elucidating the underlying principles of their stability and re-folding on biological timescales. Here, to investigate the neighbor interaction effects on the conformational propensities of amino-acids, we carried out 1 H NMR experiments for a comprehensive set of blocked dipeptides and measured the scalar coupling constants between alpha protons and amide protons as well as their chemical shifts. Detailed inspection of these NMR properties shows that, irrespective of amino-acid side-chain properties, the distributions of the measured coupling constants and chemical shifts of the dipeptides are comparatively narrow, indicating small variances of their conformation distributions. They are further compared with those of blocked amino-acids (Ac–X–NHMe), oligopeptides (Ac–GGXGG–NH 2 ), and native (lysozyme), denatured (lysozyme and outer membrane protein X from Escherichia coli), unstructured (Domain 2 of the protein 5A of Hepatitis C virus), and intrinsically disordered (hNlg3cyt: intracellular domain of human NL3) proteins. These comparative investigations suggest that the conformational preferences and local solvation environments of the blocked dipeptides are quite similar to not only those of other short oligopeptides but also those of denatured and natively unfolded proteins.

  13. Counteraction of Trehalose on N, N-Dimethylformamide-Induced Candida rugosa Lipase Denaturation: Spectroscopic Insight and Molecular Dynamic Simulation.

    Directory of Open Access Journals (Sweden)

    Xin Yang

    Full Text Available Candida rugosa lipase (CRL has been widely used as a biocatalyst for non-aqueous synthesis in biotechnological applications, which, however, often suffers significant loss of activity in organic solvent. Experimental results show that trehalose could actively counteract the organic-solvent-induced protein denaturation, while the molecular mechanisms still don't unclear. Herein, CRL was used as a model enzyme to explore the effects of trehalose on the retention of enzymatic activity upon incubation in N,N-dimethylformamide (DMF. Results showed that both catalytic activity and conformation changes of CRL influenced by DMF solvent were inhibited by trehalose in a dose-dependent fashion. The simulations further indicated that the CRL protein unfolded in binary DMF solution, but retained the native state in the ternary DMF/trehalose system. Trehalose as the second osmolyte added into binary DMF solution decreased DMF-CRL hydrogen bonds efficiently, whereas increased the intermolecular hydrogen bondings between DMF and trehalose. Thus, the origin of its denaturing effects of DMF on protein is thought to be due to the preferential exclusion of trehalose as well as the intermolecular hydrogen bondings between trehalose and DMF. These findings suggest that trehalose protect the CRL protein from DMF-induced unfolding via both indirect and direct interactions.

  14. Yeast frataxin is stabilized by low salt concentrations: cold denaturation disentangles ionic strength effects from specific interactions.

    Directory of Open Access Journals (Sweden)

    Domenico Sanfelice

    Full Text Available Frataxins are a family of metal binding proteins associated with the human Friedreich's ataxia disease. Here, we have addressed the effect of non-specifically binding salts on the stability of the yeast ortholog Yfh1. This protein is a sensitive model since its stability is strongly dependent on the environment, in particular on ionic strength. Yfh1 also offers the unique advantage that its cold denaturation can be observed above the freezing point of water, thus allowing the facile construction of the whole protein stability curve and hence the measurement of accurate thermodynamic parameters for unfolding. We systematically measured the effect of several cations and, as a control, of different anions. We show that, while strongly susceptible to ionic strength, as it would be in the cellular environment, Yfh1 stability is sensitive not only to divalent cations, which bind specifically, but also to monovalent cations. We pinpoint the structural bases of the stability and hypothesize that the destabilization induced by an unusual cluster of negatively charged residues favours the entrance of water molecules into the hydrophobic core, consistent with the generally accepted mechanism of cold denaturation.

  15. Effect of quencher, denaturants, temperature and pH on the fluorescent properties of BSA protected gold nanoclusters

    Energy Technology Data Exchange (ETDEWEB)

    Chib, Rahul, E-mail: [Department of Cell Biology and Immunology, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107 (United States); Butler, Susan [Department of Cell Biology and Immunology, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107 (United States); Raut, Sangram [Department of Cell Biology and Immunology, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107 (United States); Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX 76129 (United States); Shah, Sunil; Borejdo, Julian [Department of Cell Biology and Immunology, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107 (United States); Gryczynski, Zygmunt [Department of Cell Biology and Immunology, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107 (United States); Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX 76129 (United States); Gryczynski, Ignacy, E-mail: [Department of Cell Biology and Immunology, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107 (United States)


    In this paper, we have synthesized BSA protected gold nanoclusters (BSA Au nanocluster) and studied the effect of quencher, protein denaturant, pH and temperature on the fluorescence properties of the tryptophan molecule of the BSA Au nanocluster and native BSA. We have also studied their effect on the peak emission of BSA Au nanoclusters (650 nm). The photophysical characterization of a newly developed fluorophore in different environments is absolutely necessary to futher develop their biomedical and analytical applications. It was observed from our experiments that the tryptophan in BSA Au nanoclusters is better shielded from the polar environment. Tryptophan in native BSA showed a red shift in its peak emission wavelength position. Tryptophan is a highly polarity sensitive dye and a minimal change in its microenvironment can be easily observed in its photophysical properties. - Highlights: • Tryptophan is easily accessible in native BSA compared to BSA Au nanoclusters. • Guanidine HCL denatures native BSA more compared to BSA Au nanoclusters. • High temperature decreases the quantum yield of tryptophan and BSA Au nanocluster. • Emission wavelength of BSA Au nanoclusters remains constant with increasing pH. • BSA Au nanoclusters are robust to the changes in their environments.

  16. Effect of quencher, denaturants, temperature and pH on the fluorescent properties of BSA protected gold nanoclusters

    International Nuclear Information System (INIS)

    Chib, Rahul; Butler, Susan; Raut, Sangram; Shah, Sunil; Borejdo, Julian; Gryczynski, Zygmunt; Gryczynski, Ignacy


    In this paper, we have synthesized BSA protected gold nanoclusters (BSA Au nanocluster) and studied the effect of quencher, protein denaturant, pH and temperature on the fluorescence properties of the tryptophan molecule of the BSA Au nanocluster and native BSA. We have also studied their effect on the peak emission of BSA Au nanoclusters (650 nm). The photophysical characterization of a newly developed fluorophore in different environments is absolutely necessary to futher develop their biomedical and analytical applications. It was observed from our experiments that the tryptophan in BSA Au nanoclusters is better shielded from the polar environment. Tryptophan in native BSA showed a red shift in its peak emission wavelength position. Tryptophan is a highly polarity sensitive dye and a minimal change in its microenvironment can be easily observed in its photophysical properties. - Highlights: • Tryptophan is easily accessible in native BSA compared to BSA Au nanoclusters. • Guanidine HCL denatures native BSA more compared to BSA Au nanoclusters. • High temperature decreases the quantum yield of tryptophan and BSA Au nanocluster. • Emission wavelength of BSA Au nanoclusters remains constant with increasing pH. • BSA Au nanoclusters are robust to the changes in their environments.

  17. Effect of neonatal sublingual vaccination with native or denatured ovalbumin and adjuvant CpG or cholera toxin on systemic and mucosal immunity in mice. (United States)

    Huang, C-F; Wu, T-C; Chu, Y-H; Hwang, K-S; Wang, C-C; Peng, H-J


    Sublingual immunotherapy has been applied for allergic diseases, but whether sublingual immunization in neonates can prevent sensitization has not been studied. In this study, we evaluate the effect of neonatal sublingual vaccination with native or denatured allergens alone or plus adjuvant on allergy prevention. Newborn BALB/c mice were sublingually vaccinated daily for the first 3 days with native or denatured ovalbumin (OVA) only, or combined adjuvant CpG or cholera toxin (CT). They were sensitized with OVA adsorbed onto alum 7 weeks after the last vaccination. Specific secretory IgA antibody responses were readily induced by neonatal vaccination with antigen plus CpG or CT, but not with antigen alone. Whereas vaccination with denatured OVA plus CpG markedly enhanced T helper 1 (Th1) responses and inhibited IgE production, vaccination with denatured OVA plus CT increased cervical lymph node cell production of interleukin-4 (IL-4), IL-5, IL-6, and serum IgG1 responses. These data demonstrate that neonatal sublingual vaccination with denatured OVA and CpG not only preferentially induces systemic Th1 responses and mucosal immunity, but also simultaneously abrogates IgE production. Neonatal sublingual vaccines may play a role for the strategy of allergy prevention.

  18. Soluble porphyrin polymers (United States)

    Gust, Jr., John Devens; Liddell, Paul Anthony


    Porphyrin polymers of Structure 1, where n is an integer (e.g., 1, 2, 3, 4, 5, or greater) ##STR00001## are synthesized by the method shown in FIGS. 2A and 2B. The porphyrin polymers of Structure 1 are soluble in organic solvents such as 2-MeTHF and the like, and can be synthesized in bulk (i.e., in processes other than electropolymerization). These porphyrin polymers have long excited state lifetimes, making the material suitable as an organic semiconductor for organic electronic devices including transistors and memories, as well as solar cells, sensors, light-emitting devices, and other opto-electronic devices.

  19. SANS studies of polymers

    International Nuclear Information System (INIS)

    Wignall, G.D.


    Before small-angle neutron scattering (SANS), chain conformation studies were limited to light and small angle x-ray scattering techniques, usually in dilute solution. SANS from blends of normal and labeled molecules could give direct information on chain conformation in bulk polymers. Water-soluble polymers may be examined in H 2 O/D 2 O mixtures using contrast variation methods to provide further information on polymer structure. This paper reviews some of the information provided by this technique using examples of experiments performed at the National Center for Small-Angle Scattering Research (NCSASR)

  20. Polymers in separation processes (United States)

    Wieszczycka, Karolina; Staszak, Katarzyna


    Application of polymer materials as membranes and ion-exchange resins was presented with a focus on their use for the recovery of metal ions from aqueous solutions. Several membrane techniques were described including reverse osmosis, nanofiltration, ultrafiltration, diffusion and Donnan dialysis, electrodialysis and membrane extraction system (polymer inclusion and supported membranes). Moreover, the examples of using ion-exchange resins in metal recovery were presented. The possibility of modification of the resin was discussed, including hybrid system with metal cation or metal oxide immobilized on polymer matrices or solvent impregnated resin.

  1. Microstructured polymer optical fibres

    CERN Document Server

    Large, Maryanne; Barton, Geoff; van Eijkelenborg, Martijn A


    Microstructured Polymer Optical Fibres describes the optical properties of microstructured fibres, how they are made and modelled, and outlines some potential applications. These applications include areas where polymer fibres are already used, such as high-data rate transmission for Fibre-to-the Home or within cars, as well as completely new areas such as the photonic bandgap transmission of ""difficult"" wavelengths. Emphasising a conceptual understanding of the underlying physics, Microstructured Polymer Optical Fibres is clearly written, and includes numerous illustrations. It provides an

  2. Biomedical applications of polymers

    CERN Document Server

    Gebelein, C G


    The biomedical applications of polymers span an extremely wide spectrum of uses, including artificial organs, skin and soft tissue replacements, orthopaedic applications, dental applications, and controlled release of medications. No single, short review can possibly cover all these items in detail, and dozens of books andhundreds of reviews exist on biomedical polymers. Only a few relatively recent examples will be cited here;additional reviews are listed under most of the major topics in this book. We will consider each of the majorclassifications of biomedical polymers to some extent, inclu

  3. Investigations into polymer and carbon nanomaterial separations (United States)

    Owens, Cherie Nicole

    utilize as novel UTLC substrates. Additionally, aligned electrospun UTLC (AE-UTLC) substrates were developed to compare to the randomly oriented electrospun (E-UTLC) devices. The PHB plates were compared to commercially available substrates for the separation of biological samples: nucleotides and steroids. The electrospun substrates show lower band broadening and higher reproducibility in a smaller development distance than commercially available TLC plates, conserving both resources and time. The AE-UTLC plates provided further enhancement of reproducibility and development time compared to E-UTLC plates. Thus, the P3HB E-UTLC phases are an excellent sustainable option for TLC as they are biodegradable and perform better than commercial phases. A third topic of interest is the study of ordered carbon nanomaterials. The typical amorphous carbon used as a stationary phase in Hypercarb ® is known to consist of basal- and edge-plane oriented sites. This heterogeneity of the stationary phase can lead to peak broadening that may be improved by using homogeneous carbon throughout. Amorphous, basal-plane, and edge-plane carbons were produced in-house through membrane template synthesis. Amorphous, basal-plane, and edge-plane carbons were then used separately as chromatographic phases in capillary electrochomatography (CEC). Differences in chromatographic performance between these species were assessed by modeling retention data for test solutes to determine Linear Solvation Energy Relationships (LSER). The LSER study for the three carbon phases indicates that the main difference is in the polarizability, and hydrogen bonding character of the surface leading to unique solute interactions. These results highlight the possible usefulness of using these phases independently.

  4. Superabsorbent polymer; Kokyushusei porima

    Energy Technology Data Exchange (ETDEWEB)

    Fujita, M. [Sanyo Kasei Kogyo K.K., Tokyo (Japan)


    Superabsorbent polymer (SAP) which has the absorbing ability from several hundreds to thousand times of the dead weight possesses many other functions in addition to the absorbing function, and studies on its application to various fields have been carried on very actively. Particularly, about 90% of the demand is for the application to body fluid absorber in the fields of sanitary materials. Basic water absorption mechanism, kinds, production methods, special features and applied cases of superabsorbent polymer are introduced. SAP is structured by loosely bridged water soluble polymer, particularly polymer electrolyte, to provide water unsoluble and water swelling properties. The kinds and production methods of SAP are described. SAP has respiration property in addition to the high water absorbing power and water holding ability. It has carboxyl ions, and has ammonia absorption ability and polyvalent metal ion adsorption ability. Paper diapers, water holding materials for soil, and cold reserving materials are discussed as examples of SAP application. 3 refs., 2 figs., 1 tab.

  5. Rheology of Supramolecular Polymers

    DEFF Research Database (Denmark)

    Shabbir, Aamir

    efficient processes or biomedical areas. Design and development of supramolecular polymers using ionic, hydrogen bonding or transition metal complexes with tailored properties requires deep understanding of dynamics both in linear and non-linear deformations. While linear rheology is important to understand...... the dynamics under equilibrium conditions, extensional rheology is relevant during the processing or in the usage of polymers utilizing supramolecular associations for example, acrylic based pressure sensitive adhesives are subjected to extensional deformations during the peeling where strain hardening......) hydrogen bonding polymers, and (b) ionic bonding polymers (hereafter termed as ionomers). We study linear and non-linear rheology fora model system of entangled pure poly(n-butyl acrylate), PnBA, homopolymer andfour poly(acrylic acid), PnBA-PAA, copolymers with varying AA side groups synthesizedvia...

  6. Conjugated Polymer Solar Cells

    National Research Council Canada - National Science Library

    Paraschuk, Dmitry Y


    This report results from a contract tasking Moscow State University as follows: Conjugated polymers are promising materials for many photonics applications, in particular, for photovoltaic and solar cell devices...

  7. Tunable Optical Polymer Systems

    National Research Council Canada - National Science Library

    Jenekhe, S. A; Bard, Allen J; Chen, S. H; Hammond, P. T; Rothberg, L. J


    This multidisciplinary university research initiative (MURI) program investigated tunable optical polymer systems suitable for large-area color-switchable coatings and devices, displays, sensors, and other electronic applications...

  8. Zwitterionic Electroactive Polymer Actuators

    National Research Council Canada - National Science Library

    Zakin, Mitchell


    .... The enabling technology is a zwitterionic polyaniline derivative in which generation of +/- charge pairs upon oxidation provides significant conformational distortion along the polymer backbone, and a concomitant change in free volume...

  9. Biocatalytic Polymer Skin Adhesives

    National Research Council Canada - National Science Library

    LeJeune, Keith


    .... Preliminary results also suggest that the incorporation of enzymes within such polymers reduces immunogenic and allergenic responses that are often observed when applying protein-based materials on skin tissue...

  10. Polymers for Protein Conjugation

    Directory of Open Access Journals (Sweden)

    Gianfranco Pasut


    Full Text Available Polyethylene glycol (PEG at the moment is considered the leading polymer for protein conjugation in view of its unique properties, as well as to its low toxicity in humans, qualities which have been confirmed by its extensive use in clinical practice. Other polymers that are safe, biodegradable and custom-designed have, nevertheless, also been investigated as potential candidates for protein conjugation. This review will focus on natural polymers and synthetic linear polymers that have been used for protein delivery and the results associated with their use. Genetic fusion approaches for the preparation of protein-polypeptide conjugates will be also reviewed and compared with the best known chemical conjugation ones.

  11. Edible Polymers: Challenges and Opportunities


    Subhas C. Shit; Pathik M. Shah


    Edible polymers have established substantial deliberation in modern eons because of their benefits comprising use as edible materials over synthetic polymers. This could contribute to the reduction of environmental contamination. Edible polymers can practically diminish the complexity and thus improve the recyclability of materials, compared to the more traditional non-environmentally friendly materials and may be able to substitute such synthetic polymers. A synthetic hydrogel polymer unlock...

  12. Reactive polymer fused deposition manufacturing (United States)

    Kunc, Vlastimil; Rios, Orlando; Love, Lonnie J.; Duty, Chad E.; Johs, Alexander


    Methods and compositions for additive manufacturing that include reactive or thermosetting polymers, such as urethanes and epoxies. The polymers are melted, partially cross-linked prior to the depositing, deposited to form a component object, solidified, and fully cross-linked. These polymers form networks of chemical bonds that span the deposited layers. Application of a directional electromagnetic field can be applied to aromatic polymers after deposition to align the polymers for improved bonding between the deposited layers.

  13. Semi-metallic polymers

    DEFF Research Database (Denmark)

    Bubnova, Olga; Khan, Zia Ullah; Wang, Hui


    Polymers are lightweight, flexible, solution-processable materials that are promising for low-cost printed electronics as well as for mass-produced and large-area applications. Previous studies demonstrated that they can possess insulating, semiconducting or metallic properties; here we report...... a Fermi glass to a semi-metal. The high Seebeck value, the metallic conductivity at room temperature and the absence of unpaired electron spins makes polymer semi-metals attractive for thermoelectrics and spintronics....

  14. Graphene-polymer composites (United States)

    Carotenuto, G.; Romeo, V.; Cannavaro, I.; Roncato, D.; Martorana, B.; Gosso, M.


    Graphene is a novel nanostructured material that can be conveniently used as filler for thermoplastic polymers or thermosetting resins, and the resulting nanocomposite material has unique mechanical and chemical/physical properties. Industrial production of graphene/polymer materials requires the availability of a chemical route to produce massive amount of graphene. Natural graphite flakes can be the best starting material for a bulk-production of graphene to be used in the polymeric nanocomposite preparation.

  15. Sulfur polymer cement concrete

    International Nuclear Information System (INIS)

    Weber, H.H.; McBee, W.C.


    Sulfur-based composite materials formulated using sulfur polymer cement (SPC) and mineral aggregates are described and compared with conventional portland cement based materials. Materials characteristics presented include mechanical strength, chemical resistance, impact resistance, moisture permeation, and linear shrinkage during placement and curing. Examples of preparation and placement of sulfur polymer cement concrete (SC) are described using commercial scale equipment. SC applications presented are focused into hostile chemical environments where severe portland cement concrete (PCC) failure has occurred

  16. Interfaced conducting polymers

    Czech Academy of Sciences Publication Activity Database

    Stejskal, Jaroslav; Bober, Patrycja; Trchová, Miroslava; Nuzhnyy, Dmitry; Bovtun, Viktor; Savinov, Maxim; Petzelt, Jan; Prokeš, J.


    Roč. 224, February (2017), s. 109-115 ISSN 0379-6779 R&D Projects: GA ČR(CZ) GA16-02787S Institutional support: RVO:61389013 ; RVO:68378271 Keywords : polyaniline * polypyrrole * poly(p-phenylenediamine) Subject RIV: CD - Macromolecular Chemistry; CD - Macromolecular Chemistry (FZU-D) OBOR OECD: Polymer science; Polymer science (FZU-D) Impact factor: 2.435, year: 2016

  17. Virus Infection Triggers MAVS Polymers of Distinct Molecular Weight

    Directory of Open Access Journals (Sweden)

    Natalia Zamorano Cuervo


    Full Text Available The mitochondrial antiviral signaling (MAVS adaptor protein is a central signaling hub required for cells to mount an antiviral response following virus sensing by retinoic acid-inducible gene I (RIG-I-like receptors. MAVS localizes in the membrane of mitochondria and peroxisomes and in mitochondrial-associated endoplasmic reticulum membranes. Structural and functional studies have revealed that MAVS activity relies on the formation of functional high molecular weight prion-like aggregates. The formation of protein aggregates typically relies on a dynamic transition between oligomerization and aggregation states. The existence of intermediate state(s of MAVS polymers, other than aggregates, has not yet been documented. Here, we used a combination of non-reducing SDS-PAGE and semi-denaturing detergent agarose gel electrophoresis (SDD-AGE to resolve whole cell extract preparations to distinguish MAVS polymerization states. While SDD-AGE analysis of whole cell extracts revealed the formation of previously described high molecular weight prion-like aggregates upon constitutively active RIG-I ectopic expression and virus infection, non-reducing SDS-PAGE allowed us to demonstrate the induction of lower molecular weight oligomers. Cleavage of MAVS using the NS3/4A protease revealed that anchoring to intracellular membranes is required for the appropriate polymerization into active high molecular weight aggregates. Altogether, our data suggest that RIG-I-dependent MAVS activation involves the coexistence of MAVS polymers with distinct molecular weights.

  18. Electrophoresis of Ion Containing Polymers in Microfluidic Applications (United States)

    Chow, Andrea


    Microfluidic technology offers the benefits of miniaturization, integration, and automation that can lead to faster analysis with higher data quality and higher sample throughput. One of the first microfluidic systems commercialized is for biomolecular sizing using the principles of gel electrophoresis. In these chips, the microchannels are filled with a polymer solution at a concentration above the entanglement threshold. For DNA and RNA sizing, the procedures of sample injection, fluorescent dye staining of the analyte, electrophoretic separation by size, and optical detection of size fractions are integrated. These microchip analyses are similar to those performed in conventional capillary electrophoresis, except that the analysis times are usually an order of magnitude shorter. For protein sizing in sodium dodecyl sulphate (SDS) micelle solutions in which the proteins are denatured, an additional step of protein destaining is also integrated onto the chip, enabling an application that has no simple analog in conventional capillary electrophoresis. The scaling laws based on polymer physics considerations dictating the sizing mechanisms and separation efficiencies for these microfluidic applications will be discussed.

  19. Purification of correctly oxidized MHC class I heavy-chain molecules under denaturing conditions: a novel strategy exploiting disulfide assisted protein folding

    DEFF Research Database (Denmark)

    Ferré, Henrik; Ruffet, Emmanuel; Blicher, Thomas


    with correct disulfide bonding are formed under non-reducing denaturing conditions and separated from scrambled disulfide bond forms by hydrophobic interaction chromatography. In the second step, rapid refolding of the oxidized heavy chains is afforded by disulfide bond-assisted folding in the presence of beta......The aim of this study has been to develop a strategy for purifying correctly oxidized denatured major histocompability complex class I (MHC-I) heavy-chain molecules, which on dilution, fold efficiently and become functional. Expression of heavy-chain molecules in bacteria results in the formation...... of insoluble cellular inclusion bodies, which must be solubilized under denaturing conditions. Their subsequent purification and refolding is complicated by the fact that (1). correct folding can only take place in combined presence of beta(2)-microglobulin and a binding peptide; and (2). optimal in vitro...

  20. On-line two-step stacking in capillary zone electrophoresis for the preconcentration of strychnine and brucine. (United States)

    Yang, Xiumin; Zhang, Shuaihua; Wang, Juntao; Wang, Chun; Wang, Zhi


    An on-line sample preconcentration method by two-step stacking i.e., sweeping and micelle to solvent stacking, in capillary zone electrophoresis (CZE) has been developed for the determination of strychnine and brucine in traditional Chinese herbal medicines. After experimental optimizations, the best separation was achieved by using 75 mM phosphate buffer (pH 2.5) with 30% methanol (v/v). Compared with normal CZE injection, 51- and 38-fold improvement in concentration sensitivity was achieved for strychnine and brucine, respectively. The calibration curve was linear in the range of 0.1-5.0 μg mL(-1) for both strychnine and brucine, with the correlation coefficients of 0.9998 and 0.9997, respectively. The limits of detection (S/N=3) for both alkaloids were 0.01 μg mL(-1). The inter-day (n=8) and intra-day (n=5) reproducibilities expressed as the relative standard deviations for corrected peak area were less than 9.5%. The method was applied to determine strychnine and brucine in two Chinese herbal medicines, with recoveries ranging from 94.2% to 105.4%. The results indicated that the method is simple, rapid, reliable, and can be applied to determine strychnos alkaloids in traditional Chinese herbal medicines. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. [Preparation of new hydrophilic monolithic columns and their applications in capillary liquid chromatography and pressurized capillary electrochromatography]. (United States)

    Gao, Ye; Wang, Yan; Wang, Chaoran; Gu, Xue; Yan, Chao


    New hydrophilic monolithic columns were prepared with {[3-(methacryloylamino) propyl] dimethyl(3-sulfopropyl)ammonium hydroxide inner salt (SPP)} as monomer, pentaerythritol triacrylate (PETA) as crosslinking agent, azobisisobutyronitrile (AIBN) as initiator with two different porogens consisting of ethanol/ethylene glycol and methanol/1 ,4-butanediol, separately. In order to obtain monolithic columns with satisfactory efficiency, electroosmotic flow (EOF) velocity and permeability, the contents of the polymerization mixture were investigated and optimized. The performances of the two columns were compared in the permeability and separation performance. It was found that the monolithic column prepared with ethanol/ ethylene glycol had a better column efficiency and selectivity than that with methanol/1,4-butanediol, but was inferior to the latter in permeability. The effect of salt concentration (from 10 to 70 mmol/L ammonium formate) on the retention of nucleosides was investigated. It was observed that the retention factors of these nucleosides increased at first and then decreased. The columns were used in capillary liquid chromatography (cLC) and pressurized capillary electrochromatography (pCEC) for the separation of a test mixture of amines, phenols and nucleosides separately, and satisfactory separations for these samples were achieved. The column used in pCEC system showed better separation and higher speed of the mixture consisted of phenols and nucleosides compared to those used in cLC system.

  2. Nicotine-evoked cytosolic Ca2+ increase and cell depolarization in capillary endothelial cells of the bovine adrenal medulla

    Directory of Open Access Journals (Sweden)



    Full Text Available Endothelial cells are directly involved in many functions of the cardiovascular system by regulating blood flow and blood pressure through Ca2+ dependent exocitosis of vasoactive compounds. Using the Ca2+ indicator Fluo-3 and the patch-clamp technique, we show that bovine adrenal medulla capillary endothelial cells (B AMCECs respond to acetylcholine (ACh with a cytosolic Ca2+ increase and depolarization of the membrane potential (20.3±0.9 mV; n=23. The increase in cytosolic Ca2+ induced by 10µM ACh was mimicked by the same concentration of nicotine but not by muscarine and was blocked by 100 µM of hexamethonium. On the other hand, the increase in cytosolic Ca2+ could be depressed by nifedipine (0.01 -100 µM or withdrawal of extracellular Ca2+. Taken together, these results give evidence for functional nicotinic receptors (nAChRs in capillary endothelial cells of the adrenal medulla. It suggests that nAChRs in B AMCECs may be involved in the regulation of the adrenal gland's microcirculation by depolarizing the membrane potential, leading to the opening of voltage-activated Ca2+ channels, influx of external Ca2+ and liberation of vasoactive compounds.

  3. Investigation of maltodextrin-based synergistic system with amino acid chiral ionic liquid as additive for enantioseparation in capillary electrophoresis. (United States)

    Chen, Jiaquan; Du, Yingxiang; Sun, Xiaodong


    The combined use of chiral ionic liquids (ILs) and chiral selectors in capillary electrophoresis (CE) to establish a synergistic system has proven to be an effective approach for enantioseparation. In this article, tetramethylammonium-L-arginine, a kind of amino acid chiral IL, was applied to investigate its potential synergistic effect with maltodextrin in CE enantioseparation. The established maltodextrin-based synergistic system showed markedly improved enantioseparations compared with the single maltodextrin system. Parameters such as the chiral IL concentration, maltodextrin concentration, buffer pH, applied voltage, and capillary temperature were optimized. Satisfactory enantioseparation of the five studied drugs, including nefopam, duloxetine, ketoconazole, cetirizine, and citalopram was achieved in 50 mM Tris-H 3 PO 4 buffer solution (pH 3.0) containing 7.0% (m/v) maltodextrin and 60 mM tetramethylammonium-L-arginine. In addition, the chiral configuration of tetramethylammonium-L-arginine was also investigated to demonstrate the existence of a synergistic effect between chiral ILs and maltodextrin. © 2017 Wiley Periodicals, Inc.

  4. Application of a low impedance contactless conductometric detector for the determination of inorganic cations in capillary monolithic column chromatography. (United States)

    Shen, Dazhong; Li, Dongdong; Yang, Xiuwen; Zhu, Yan; Dong, Jianfeng; Kang, Qi


    Poly(glycidyl methacrylate) cation exchange monolithic column was prepared in fused-silica capillaries of 320 μm i.d. by thermally initiated radical polymerization and utilized in capillary ion chromatography. With 15 mM methanesulfonic acid as the mobile phase, the separations of a mixture of inorganic cations (Li(+), Na(+), NH(4)(+), K(+)) was tested by using a capacitively coupled contactless conductivity detector (C(4)D) and a low impedance C(4)D (LIC(4)D). The LIC(4)D is the series combination of a C(4)D and a quartz crystal resonator. At the resonant frequency of the series combination, the capacitor impedance from capillary wall was offset by the inductance impedance from the quartz crystal resonator. A minimum impedance was obtained in the impedance-frequency curve of the combination. The responses of the C(4)D and LIC(4)D were analyzed based on an equivalent circuit model. It was shown that the sensitivity of the C(4)D to the change in analyte concentration is rather poor due to the high ratio of the impedance from the capillary wall capacitor to the solution impedance. The LIC(4)D has the similar sensitivity as a contact conductivity detector but a much smaller cell volume. The on-column detection model was realized by LiC(4)D without preparation of optical detection window in monolithic column. Copyright © 2010 Elsevier B.V. All rights reserved.

  5. Rapid Polymer Sequencer (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)


    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  6. Crystallization in polymer nanocomposites (United States)

    Chrissopoulou, Kyriakh; Perivolari, Helena; Leisch, Stefanos; Papananou, Hellen; Anastasiadis, Spiros H.

    Polymer crystallization is a very interesting topic since it is responsible for the final properties of the materials. On the other hand, addition of inorganic nanomaterials has been recently widely used to optimize polymer properties. In this work, the effect of the presence of surfaces and of the severe confinement on polymer morphology and crystallization are investigated in hydrophilic nanohybrids of poly(ethylene oxide) and silica nanoparticles of different sizes; hybrids with different ratios of the two kinds of nanoparticles were synthesized as well, to achieve the highest confinement. Differential Scanning Calorimetry (DSC) and X-Ray Diffraction (XRD) were utilized to investigate the behavior and showed that the polymer chains that were able to crystallize showed a different crystalline behavior in the hybrids with lower Tm and lower crystallinity. Under severe confinement polymer crystallization was completely suppressed. Moreover, the crystallization kinetics was investigated with Isothermal Polarized Optical Microscopy (POM) and Isothermal Differential Scanning Calorimetry (DSC) showing different characteristics in the hybrids compared to that of the neat polymer depending on the silica content. Sponsored by the Greek GSRT (AENAO research project, Action KRIPIS)

  7. 40 CFR 723.250 - Polymers. (United States)


    ..., boron, phosphorus, titanium, manganese, iron, nickel, copper, zinc, tin, and zirconium. (3) Polymers... introduce into the polymer elements, properties, or functional groups that would render the polymer...

  8. Simulations of Polymer Translocation (United States)

    Vocks, H.


    Transport of molecules across membranes is an essential mechanism for life processes. These molecules are often long, and the pores in the membranes are too narrow for the molecules to pass through as a single unit. In such circumstances, the molecules have to squeeze -- i.e., translocate -- themselves through the pores. DNA, RNA and proteins are such naturally occuring long molecules in a variety of biological processes. Understandably, the process of translocation has been an active topic of current research: not only because it is a cornerstone of many biological processes, but also due to its relevance for practical applications. Translocation is a complicated process in living organisms -- the presence of chaperone molecules, pH, chemical potential gradients, and assisting molecular motors strongly influence its dynamics. Consequently, the translocation process has been empirically studied in great variety in biological literature. Study of translocation as a biophysical process is more recent. Herein, the polymer is simplified to a sequentially connected string of N monomers as it passes through a narrow pore on a membrane. The quantities of interest are the typical time scale for the polymer to leave a confining cell (the ``escape of a polymer from a vesicle'' time scale), and the typical time scale the polymer spends in the pore (the ``dwell'' time scale) as a function of N and other parameters like membrane thickness, membrane adsorption, electrochemical potential gradient, etc. Our research is focused on computer simulations of translocation. Since our main interest is in the scaling properties, we use a highly simplified description of the translocation process. The polymer is described as a self-avoiding walk on a lattice, and its dynamics consists of single-monomer jumps from one lattice site to another neighboring one. Since we have a very efficient program to simulate such polymer dynamics, which we decribe in Chapter 2, we can perform long

  9. Precursor polymer compositions comprising polybenzimidazole

    Energy Technology Data Exchange (ETDEWEB)

    Klaehn, John R.; Peterson, Eric S.; Orme, Christopher J.


    Stable, high performance polymer compositions including polybenzimidazole (PBI) and a melamine-formaldehyde polymer, such as methylated, poly(melamine-co-formaldehyde), for forming structures such as films, fibers and bulky structures. The polymer compositions may be formed by combining polybenzimidazole with the melamine-formaldehyde polymer to form a precursor. The polybenzimidazole may be reacted and/or intertwined with the melamine-formaldehyde polymer to form the polymer composition. For example, a stable, free-standing film having a thickness of, for example, between about 5 .mu.m and about 30 .mu.m may be formed from the polymer composition. Such films may be used as gas separation membranes and may be submerged into water for extended periods without crazing and cracking. The polymer composition may also be used as a coating on substrates, such as metal and ceramics, or may be used for spinning fibers. Precursors for forming such polymer compositions are also disclosed.

  10. Confined relaxations of grafted polymer in solutions of linear polymer (United States)

    Poling-Skutvik, Ryan; Krishnamoorti, Ramanan; Conrad, Jacinta

    Using neutron spin echo spectroscopy (NSE), we investigate the relaxations of polymer grafted to silica nanoparticles dispersed in semidilute solutions of linear polymer. The grafted polymer has a radius of gyration comparable to radius of the silica nanoparticle with a moderate grafting density so that the grafted polymer is more extended than a Gaussian chain. On length scales ranging from 1 to 20 nm and time scales less than 100 ns, the dynamics of the grafted polymer deviate from the standard Zimm model derived for linear polymers. Instead, the polymer chains are confined and unable to fully relax over the experimental time. The confinement length agrees with the distance between chains decreases as the linear polymer concentration is increased. Additionally, the confinement length is independent of linear polymer molecular weight, suggesting that linear polymer cannot penetrate the grafted layer. Instead, the grafted chains collapse onto themselves, similar to the structural changes observed in systems of star and linear polymers at high concentrations of linear polymer. We verify this physical picture using small-angle x-ray scattering and atomic force microscopy to observe aggregation of grafted particles at high concentrations of linear polymer.

  11. Effect of Quencher, Denaturants, Temperature and pH on the Fluorescent Properties of BSA Protected Gold Nanoclusters. (United States)

    Chib, Rahul; Butler, Susan; Raut, Sangram; Shah, Sunil; Borejdo, Julian; Gryczynski, Zygmunt; Gryczynski, Ignacy


    In this paper, we have synthesized BSA protected gold nanoclusters (BSA Au nanocluster) and studied the effect of quencher, protein denaturant, pH and temperature on the fluorescence properties of the tryptophan molecule of the BSA Au nanocluster and native BSA. We have also studied their effect on the peak emission of BSA Au nanoclusters (650 nm). The phtophysical characterization of a newly developed fluorophore in different environments is absolutely necessary to futher develop their biomedical and analytical applications. It was observed from our experiments that the tryptophan in BSA Au nanoclusters is better shielded from the polar environment. Tryptophan in native BSA showed a red shift in its peak emission wavelength position. Tryptophan is a highly polarity sensitive dye and a minimal change in its microenvironment can be easily observed in its photophysical properties.

  12. Polymerase chain reaction and denaturing gradient gel electrophoresis monitoring of fecal bifidobacterium populations in a prebiotic and probiotic feeding trial. (United States)

    Satokari, R M; Vaughan, E E; Akkermans, A D; Saarela, M; De Vos, W M


    A culture-independent approach based on genus-specific PCR and denaturing gradient gel electrophoresis (DGGE) was used to monitor qualitative changes in fecal bifidobacterial communities in a human feeding trial. DNA was extracted directly from feces and bifidobacterial 16S rDNA sequences were amplified using genus-specific PCR. The PCR fragments were subsequently separated in a sequence-specific manner by DGGE in order to obtain a profile of bifidobacterial fragments. The DGGE profiles revealed that in general, administration for two weeks of galactooligosaccharide and/or Bifidobacterium lactis Bb-12 (8 g and 3 x 10(10) cfu per day, respectively) did not affect the qualitative composition of the indigenous Bifidobacterium population, while B. lactis Bb-12 transiently colonised the gut.

  13. The detection of Mycoplasma (formerly Eperythrozoon) wenyonii by 16S rDNA PCR and denaturing gradient gel electrophoresis. (United States)

    McAuliffe, Laura; Lawes, Joanna; Bell, Suzanna; Barlow, Alex; Ayling, Roger; Nicholas, Robin


    Although the role of Mycoplasma wenyonii in disease is still subject to some debate, infections have been reported to result in parasitaemia, anaemia, scrotal and hind limb oedema, tachycardia, pyrexia, infertility, swollen teats, prefemoral lymphadenopathy and decreased milk production. Previously, diagnosis of M. wenyonii has been based on blood smears but is not specific for M. wenyonii and can be difficult to interpret. We have previously described the use of PCR and denaturing gradient gel electrophoresis (DGGE) for the detection and differentiation of Mycoplasma species. DGGE enables the rapid and specific identification of Mycoplasma species and is ideally suited to detecting both mixed infections and new and unusual species. In this study, we have used DGGE with universal primers to detect M. wenyonii DNA from blood samples. DGGE can be used on blood samples as a rapid and specific test for M. wenyonii and can also be used as a screening test for other blood borne pathogens.

  14. Comparison of bacterial community changes in fermenting kimchi at two different temperatures using a denaturing gradient gel electrophoresis analysis. (United States)

    Hong, Yeun; Yang, Hee-Seok; Chang, Hae-Choon; Kim, Hae-Yeong


    A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique followed by sequencing of the 16S rDNA fragments eluted from the bands of interest on denaturing gradient gels was used to monitor changes in the bacterial microflora of two commercial kimchi, salted cabbage, and ingredient mix samples during 30 days of fermentation at 4°C and 10°C. Leuconostoc (Lc.) was the dominant lactic acid bacteria (LAB) over Lactobacillus (Lb.) species at 4°C. Weissella confusa was detected in the ingredient mix and also in kimchi samples throughout fermentation in both samples at 4°C and 10°C. Lc. gelidum was detected as the dominant LAB at 4°C in both samples. The temperature affected the LAB profile of kimchi by varing the pH, which was primarily caused by the temperature-dependent competition among different LAB species in kimchi. At 4°C, the sample variations in pH and titratable acidity were more conspicuous owing to the delayed growth of LAB. Temperature affected only initial decreases in pH and initial increases in viable cell counts, but affected both the initial increases and final values of titratable acidity. The initial microflora in the kimchi sample was probably determined by the microflora of the ingredient mix, not by that of the salted cabbage. The microbial distributions in the samples used in this study resembled across the different kimchi samples and the different fermentation temperatures as the numbers of LAB increased and titratable acidity decreased.

  15. Thermal and chemical denaturation of Colocasia esculenta tuber agglutinin from α2β2to unfolded state. (United States)

    Biswas, Himadri; Chattopadhyaya, Rajagopal


    The major tuber storage protein of Colocasia esculenta, is a monocot mannose-binding, widely used dietary lectin, containing two polypeptides of 12.0 and 12.4 kDa. By both gel filtration and dynamic light scattering at pH 7.2, the lectin has a α 2 β 2 form of apparent molecular mass of 48.2 kDa and a hydrodynamic radius of 6.1 ± .2 nm; however, at pH 3, it migrates as αβ and has a reduced hydrodynamic radius of 4.6 ± .3 nm. Our circular dichroism spectroscopy studies show that the lectin retains approximately 100% of its secondary structure between pH 2-8, going down to ~90% for extreme acidic/alkaline conditions. The fluorescence emission maxima of 346 to 350 nm for pH 4 to 10 show that the tryptophan residues are relatively exposed. The unfolding is a simple two-state process, N 4 ↔ 4U, as seen in our denaturation scan profiles. These denaturation profiles, monitored separately by fluorescence, far-UV CD, and near-UV CD, are completely super imposable. Analyses of these profiles provide an estimate of several thermodynamic parameters at each guanidinium chloride concentration, including the melting temperature T g , which is 346.9 K in 0 M, but lowers to 321.8 K in 3.6 M. Dimeric and tetrameric interfaces observed in the crystal structure for the same protein are used to rationalize solution data in some detail.

  16. Utilization of denaturing gradient gel electrophoresis for diagnosis of {beta}-thalassemia and ascertainment of new mutations

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, K.Y.; Liu, D.; Lee, J. [Univ. of California, San Diego (United States)] [and others


    During the past two years we have tested 2,300 Southeast Asians for alpha- and beta-thaleassemia mutations. We found the incidence of hemoglobin E ({beta}{sup 26}) to be 47% among Laotians and 38% among Cambodians. The incidence of beta thalassemia trait is 9% for Laotians and 6% for Cambodians. Thus, the risk for hemoglobin E/{beta}{sup 26} thalassemia, a transfusion-dependent disorder, is increased in these two population groups. Denaturing gradient gel electrophoresis (DGGE) has proven to be useful in testing for beta-thalassemia carriers and identifying new mutations in the beta globin gene. DNA was extracted from venous blood obtained from patients with elevated Hgb A2 (>4%). Five DNA fragments, encompassing the beta globin gene cluster, were amplified by PCR and analyzed, along with known beta gene mutations as controls, by DGGE using different denaturing gradient concentrations. Different mutations at the same nucleotide position can be distinguished by migration pattern on the DGGE (e.g., in IVS-I-1, G{r_arrow}A and T). Compound heterozygotes for {beta}-thalassemia can be detected on the same gel (e.g., HbE/mutation codon 17). New mutations are identified by their migration pattern compared with controls and determined by subsequent sequencing. We have identified three new mutations: codon 82 CAA{r_arrow}AAA in one Cambodian patient; IVS-II-667, T{r_arrow}C and IVS-II-672, A{r_arrow}C in two Laotian patients. When the parent`s genotypes are known, prenatal diagnosis can be obtained within 24 hours. Thus, PCR/DGGE combination is a rapid and reliable diagnostic approach to clinically significant {beta}-thalassemia. The most important steps are carefully designed primers and predetermined gradient concentrations for DGGE.

  17. Piezoresistance in Polymer Nanocomposites (United States)

    Rizvi, Reza

    Piezoresistivity in conductive polymer nanocomposites occurs because of the disturbance of particle networks in the polymer matrix. The piezoresistance effect becomes more prominent if the matrix material is compliant making these materials attractive for applications that require flexible force and displacement sensors such as e-textiles and biomechanical measurement devices. However, the exact mechanisms of piezoresistivity including the relationship between the matrix polymer, conductive particle, internal structure and the composite's piezoresistance need to be better understood before it can be applied for such applications. The objective of this thesis is to report on the development of conductive polymer nanocomposites for use as flexible sensors and electrodes. Electrically conductive and piezoresistive nanocomposites were fabricated by a scalable melt compounding process. Particular attention was given to elucidating the role of matrix and filler materials, plastic deformation and porosity on the electrical conduction and piezoresistance. These effects were parametrically investigated through characterizing the morphology, electrical properties, rheological properties, and piezoresistivity of the polymer nanocomposites. The electrical and rheological behavior of the nanocomposites was modeled by the percolation-power law. Furthermore, a model was developed to describe the piezoresistance behavior during plastic deformation in relation to the stress and filler concentration.

  18. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn


    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  19. Multifunctional Polymer Nanocomposites (United States)

    Galaska, Alexandra Maria; Song, Haixiang; Guo, Zhanhu

    With more awareness of energy conversion/storage and saving, different strategies have been developed to utilize the sustainable and renewable energy. Introducing nanoscale fillers can make inert polymer matrix possess unique properties to satisfy certain functions. For example, alumina nanoparticles have strengthened the weak thermosetting polymers. A combined mixture of carbon nanofibers and magnetite nanoparticles have made the inert epoxy sensitive for magnetic field for sensing applications. Introducing silica nanoparticles into conductive polymers such as polyaniline has enhanced the giant magnetoresistance behaviors. The introduced nanoparticles have made the transparent polymer have the electromagnetic interference (EMI) shielding function while reduce the density significantly. With the desired miniaturization, the materials combining different functionalities have become importantly interesting. In this talk, methodologies to prepare nanocomposites and their effects on the produced nanocomposites will be discussed. A variety of advanced polymer nanocomposites will be introduced. Unique properties including mechanical, electrical, magnetoresistance etc. and the applications for environmental remediation, energy storage/saving, fire retardancy, electromagnetic interference shielding, and electronic devices will be presented.

  20. New separation and detection methods in capillary electrophoresis and ion chromatography for the analysis of ionic compounds

    International Nuclear Information System (INIS)

    Mayrhofer, K.


    the total time for an analysis of a sample was 7 minutes. Additionally the recoveries of the inorganic anions and organic acids were determinated by spiking the samples. It was found that especially fluoride and phosphate adsorb to the pigments of the electro-dip coats because the recoveries of these ions were dependend on the concentration. The second part of the thesis deals with contactless conductivity detection in capillary electrophoresis. It was shown that the contactless conductivity detector, which was invented in 1997 at the Institute of Analytical Chemistry and Radiochemistry of the University Innsbruck, enables the sensitive detection of ions in capillary electrophoresis. Low detection limits were measured in fused silica capillaries with an inner diameter of 75 μm, e.g. 10 μg/l for fluoride and lithium. Additionally a model for explaining the principle of detector was developed. It was also shown that the contactless conductivity detector is appropriate for the analyses of cations and anions in real samples, e.g. drinking water, blood. Last but not least the conductivity detector was applied successfully to ion chromatography. Similar detection sensitivities were achieved as in commercially available conductivity detectors. (author)

  1. Efficient Xerographic Photoreceptors from Conjugated Polymers and Polymer Blends

    National Research Council Canada - National Science Library

    Zhang, Xuejun, Ph.D


    Bilayer xerographic photoreceptors in which pi-conjugated polymers and binary conjugated polymer blends are used as the charge generation layer have been fabricated, evaluated, and shown to be highly efficient...

  2. Pulsed lasers versus continuous light sources in capillary electrophoresis and fluorescence detection studies: Photodegradation pathways and models. (United States)

    Boutonnet, Audrey; Morin, Arnaud; Petit, Pierre; Vicendo, Patricia; Poinsot, Véréna; Couderc, François


    Pulsed lasers are widely used in capillary electrophoresis (CE) studies to provide laser induced fluorescence (LIF) detection. Unfortunately pulsed lasers do not give linear calibration curves over a wide range of concentrations. While this does not prevent their use in CE/LIF studies, the non-linear behavior must be understood. Using 7-hydroxycoumarin (7-HC) (10-5000 nM), Tamra (10-5000 nM) and tryptophan (1-200 μM) as dyes, we observe that continuous lasers and LEDs result in linear calibration curves, while pulsed lasers give polynomial ones. The effect is seen with both visible light (530 nm) and with UV light (355 nm, 266 nm). In this work we point out the formation of byproducts induced by pulsed laser upon irradiation of 7-HC. Their separation by CE using two Zeta LIF detectors clearly shows that this process is related to the first laser detection. All of these photodegradation products can be identified by an ESI-/MS investigation and correspond to at least two 7HC dimers. By using the photodegradation model proposed by Heywood and Farnsworth (2010) and by taking into account the 7-HC results and the fact that in our system we do not have a constant concentration of fluorophore, it is possible to propose a new photochemical model of fluorescence in LIF detection. The model, like the experiment, shows that it is difficult to obtain linear quantitation curves with pulsed lasers while UV-LEDs used in continuous mode have this advantage. They are a good alternative to UV pulsed lasers. An application involving the separation and linear quantification of oligosaccharides labeled with 2-aminobezoic acid is presented using HILIC and LED (365 nm) induced fluorescence. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Doped Chiral Polymer Metamaterials (United States)

    Park, Cheol (Inventor); Kang, Jin Ho (Inventor); Gordon, Keith L. (Inventor); Sauti, Godfrey (Inventor); Lowther, Sharon E. (Inventor); Bryant, Robert G. (Inventor)


    Some implementations provide a composite material that includes a first material and a second material. In some implementations, the composite material is a metamaterial. The first material includes a chiral polymer (e.g., crystalline chiral helical polymer, poly-.gamma.-benzyl-L-glutamate (PBLG), poly-L-lactic acid (PLA), polypeptide, and/or polyacetylene). The second material is within the chiral polymer. The first material and the second material are configured to provide an effective index of refraction value for the composite material of 1 or less. In some implementations, the effective index of refraction value for the composite material is negative. In some implementations, the effective index of refraction value for the composite material of 1 or less is at least in a wavelength of one of at least a visible spectrum, an infrared spectrum, a microwave spectrum, and/or an ultraviolet spectrum.

  4. Active Polymer Gel Actuators

    Directory of Open Access Journals (Sweden)

    Shuji Hashimoto


    Full Text Available Many kinds of stimuli-responsive polymer and gels have been developed and applied to biomimetic actuators or artificial muscles. Electroactive polymers that change shape when stimulated electrically seem to be particularly promising. In all cases, however, the mechanical motion is driven by external stimuli, for example, reversing the direction of electric field. On the other hand, many living organisms can generate an autonomous motion without external driving stimuli like self-beating of heart muscles. Here we show a novel biomimetic gel actuator that can walk spontaneously with a wormlike motion without switching of external stimuli. The self-oscillating motion is produced by dissipating chemical energy of oscillating reaction. Although the gel is completely composed of synthetic polymer, it shows autonomous motion as if it were alive.

  5. Flame spraying of polymers

    International Nuclear Information System (INIS)

    Varacalle, D.J. Jr.; Zeek, D.P.; Couch, K.W.; Benson, D.M.; Kirk, S.M.


    Statistical design-of-experiment studies of the thermal spraying of polymer powders are presented. Studies of the subsonic combustion (i.e., Flame) process were conducted in order to determine the quality and economics of polyester and urethane coatings. Thermally sprayed polymer coatings are of interest to several industries for anticorrosion applications, including the chemical, automotive, and aircraft industries. In this study, the coating design has been optimized for a site-specific application using Taguchi-type fractional-factorial experiments. Optimized coating designs are presented for the two powder systems. A substantial range of thermal processing conditions and their effect on the resultant polymer coatings is presented. The coatings were characterized by optical metallography, hardness testing, tensile testing, and compositional analysis. Characterization of the coatings yielded the thickness, bond strength, Knoop microhardness, roughness, deposition efficiency, and porosity. Confirmation testing was accomplished to verify the coating designs

  6. Nanostructured silicate polymer concrete

    Directory of Open Access Journals (Sweden)

    Figovskiy Oleg L'vovich


    Full Text Available It has been known that acid-resistant concretes on the liquid glass basis have high porosity (up to 18~20 %, low strength and insufficient water resistance. Significant increasing of silicate matrix strength and density was carried out by incorporation of special liquid organic alkali-soluble silicate additives, which block superficial pores and reduce concrete shrinkage deformation. It was demonstrated that introduction of tetrafurfuryloxisilane additive sharply increases strength, durability and shock resistance of silicate polymer concrete in aggressive media. The experiments showed, that the strength and density of silicate polymer concrete increase in case of decreasing liquid glass content. The authors obtained optimal content of silicate polymer concrete, which possesses increased strength, durability, density and crack-resistance. Diffusive permeability of concrete and its chemical resistance has been investigated in various corroding media.

  7. Conductivity behaviour of polymer gel electrolytes: Role of polymer

    Indian Academy of Sciences (India)


    Abstract. Polymer is an important constituent of polymer gel electrolytes along with salt and solvent. The salt provides ions for conduction and the solvent helps in the dissolution of the salt and also provides the medium for ion conduction. Although the polymer added provides mechanical stability to the electrolytes yet.

  8. Investigation of thermal denaturation of barley nonspecific lipid transfer protein 1 (ns-LTP1b) by nuclear magnetic resonance and differential scanning calorimetry

    Czech Academy of Sciences Publication Activity Database

    Matejková, M.; Žídková, Jitka; Žídek, L.; Wimmerová, M.; Chmelík, Josef; Sklenář, V.


    Roč. 57, č. 18 (2009), s. 8444-8452 ISSN 0021-8561 R&D Projects: GA MŠk 1M0570 Institutional research plan: CEZ:AV0Z40310501 Keywords : ns-LTP1 * thermal denaturation * barley Subject RIV: CB - Analytical Chemistry , Separation Impact factor: 2.469, year: 2009

  9. The recognition of adsorbed and denatured proteins of different topographies by β2 integrins and effects on leukocyte adhesion and activation

    DEFF Research Database (Denmark)

    Brevig, T.; Holst, B.; Ademovic, Z.


    Leukocyte beta(2) integrins Mac-1 and p150,95 are promiscuous cell-surface receptors that recognise and mediate cell adhesion to a variety of adsorbed and denatured proteins. We used albumin as a model protein to study whether leukocyte adhesion and activation depended on the nm-scale topography ...

  10. Comparison of Fecal Methanogenic Archaeal Community Between Erhualian and Landrace Pigs Using Denaturing Gradient Gel Electrophoresis and Real-Time PCR Analysis

    NARCIS (Netherlands)

    Su, Y.; Smidt, H.; Zhu, W.Y.


    Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis (DGGE)

  11. Development and application of a selective pcr-denaturing gradient gel electrophoresis approach to detect a recently cultivated Bacillus group predominant in soil

    NARCIS (Netherlands)

    Tzeneva, V.A.; Li, Y.; Felske, A.; Vos, de W.M.; Akkermans, A.D.L.; Vaughan, E.E.; Smidt, H.


    The worldwide presence of a hitherto-nondescribed group of predominant soil microorganisms related to Bacillus benzoevorans was analyzed after development of two sets of selective primers targeting 16S rRNA genes in combination with denaturing gradient gel electrophoresis (DGGE). The high abundance

  12. Thermodynamics of protein denaturation at temperatures over 100 °C: CutA1 mutant proteins substituted with hydrophobic and charged residues. (United States)

    Matsuura, Yoshinori; Takehira, Michiyo; Joti, Yasumasa; Ogasahara, Kyoko; Tanaka, Tomoyuki; Ono, Naoko; Kunishima, Naoki; Yutani, Katsuhide


    Although the thermodynamics of protein denaturation at temperatures over 100 °C is essential for the rational design of highly stable proteins, it is not understood well because of the associated technical difficulties. We designed certain hydrophobic mutant proteins of CutA1 from Escherichia coli, which have denaturation temperatures (Td) ranging from 101 to 113 °C and show a reversible heat denaturation. Using a hydrophobic mutant as a template, we successfully designed a hyperthermostable mutant protein (Td = 137 °C) by substituting six residues with charged ones. Thermodynamic analyses of these mutant proteins indicated that the hydrophobic mutants were stabilized by the accumulation of denaturation enthalpy (ΔH) with no entropic gain from hydrophobic solvation around 100 °C, and that the stabilization due to salt bridges resulted from both the increase in ΔH from ion-ion interactions and the entropic effect of the electrostatic solvation over 113 °C. This is the first experimental evidence that has successfully overcome the typical technical difficulties.

  13. Characterization of the Native and Denatured Herceptin by ELISA and QCM using a High-Affinity Single Chain Fragment Variable (scFv) Recombinant Antibody (United States)

    Shang, Yuqin; Mernaugh, Ray


    Herceptin/Trastuzumab is a humanized IgG1κ light chain antibody used to treat some forms of breast cancer. A phage-displayed recombinant antibody library was used to obtain an scFv (designated 2B4) to a linear synthetic peptide representing Herceptin’s heavy chain CDR3. ELISAs and piezoimmunosensor/quartz crystal microbalance (QCM) assays were used to characterize 2B4-binding activity to both native and heat denatured Herceptin. The 2B4 scFv specifically bound to heat denatured Herceptin in a concentration dependent manner over a wide (35–220.5 nM) dynamic range. Herceptin denatures and forms significant amount of aggregates when heated. UV-Vis characterization confirms that Herceptin forms aggregates as the temperature used to heat Herceptin increases. QCM affinity assay shows that binding stoichiometry between 2B4 scFv and Herceptin follows a 1:2 relationship proving that 2B4 scFv binds strongly to the dimers of heat denatured Herceptin aggregates and exhibits an affinity constant of 7.17 × 1013 M−2. The 2B4-based QCM assay was more sensitive than the corresponding ELISA. Combining QCM with ELISA can be used to more fully characterize non-specific binding events in assays. The potential theoretical and clinical implications of these results and the advantages of using QCM to characterize human therapeutic antibodies in samples are also discussed. PMID:22934911

  14. Analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers

    NARCIS (Netherlands)

    Brons, Jolanda; van Elsas, J.D.

    To assess soil bacterial diversity, PCR systems consisting of several slightly different reverse primers together with forward primer F968-GC were used along with subsequent denaturing gradient gel electrophoresis (DGGE) or clone library analyses. In this study, a set of 13 previously used and novel

  15. Electronmicroscopical evaluation of short-term nerve regeneration through a thin-walled biodegradable poly(DLLA-epsilon-CL) nerve guide filled with modified denatured muscle tissue

    NARCIS (Netherlands)

    Meek, MF; Robinson, PH; Stokroos, [No Value; Blaauw, EH; Kors, G; den Dunnen, WFA

    The aim of this study was to evaluate short-term peripheral nerve regeneration across a 15-mm gap in the sciatic nerve of the rat, using a thin-walled biodegradable poly(DL-lactide-epsilon -caprolactone) nerve guide filled with modified denatured muscle tissue (MDMT). The evaluation was performed

  16. Evaluation of functional nerve recovery after reconstruction with a poly (DL-lactide-epsilon-caprolactone) nerve guide, filled with modified denatured muscle tissue

    NARCIS (Netherlands)

    Meek, MF; Den Dunnen, WFA; Schakenraad, JM; Robinson, PH


    The aim of this study was to compare the speed of functional nerve recovery after reconstruction with a biodegradable p(DLLA-epsilon -CL) nerve guide, as filled with either modified denatured muscle tissue (MDMT) or phosphate-buffered saline (PBS). To evaluate both motor and sensory nerve recovery,

  17. Downscaling limits and confinement effects in the miniaturization of porous polymer monoliths in narrow bore capillaries. (United States)

    Nischang, Ivo; Svec, Frantisek; Fréchet, Jean M J


    Monolithic poly(butyl methacrylate-co-ethylene dimethacrylate) columns have been prepared in capillaries ranging in inner diameter from 5 to 75 microm using thermally initiated free-radical polymerization of a mixture of butyl methacrylate, ethylene dimethacrylate, and porogens at different temperatures. Scanning electron microscopy and the measurement of hydrodynamic properties reveal that the downward scalability of the monolithic columns is greatly affected by the confinement effect of the capillary wall resulting from the decreased volume-to-surface ratio as the capillary diameter is decreased. The downscaling process is affected most by the polymerization temperature, the diffusion of the propagating radicals, and the density of coverage of polymerizable groups on the inner walls of the capillary. Optimization of all these factors enables the preparation of monolithic structures in capillaries with inner diameters as low as 5 microm while retaining the desirable properties of monoliths prepared in much larger capillaries. Under these conditions, formation of undesired dense polymer layers attached to the capillary wall was minimized. The chromatographic performance of 10, 25, and 50 microm capillaries evaluated in the reversed phase gradient separation of three proteins showed no change in elution times at identical flow velocities and gradient times, while peak elution width was the smallest with the narrowest capillary.

  18. Polymers at cryogenic temperatures

    CERN Document Server

    Fu, Shao-Yun


    Kalia and Fu's novel monograph covers cryogenic treatment, properties and applications of cryo-treated polymer materials. Written by numerous international experts, the twelve chapters in this book offer the reader a comprehensive picture of the latest findings and developments, as well as an outlook on the field. Cryogenic technology has seen remarkable progress in the past few years and especially cryogenic properties of polymers are attracting attention through new breakthroughs in space, superconducting, magnetic and electronic techniques. This book is a valuable resource for researchers, educators, engineers and graduate students in the field and at technical institutions.

  19. Mechanically Invisible Polymer Coatings

    DEFF Research Database (Denmark)


    phase comprises particles, said particles comprising a filler material and an encapsulating coating of a second polymeric material, wherein the backbones of the first and second polymeric materials are the same. The composition may be used in electroactive polymers (EAPs) in order to obtain mechanically......The present invention relates to a composition comprising encapsulated particles in a polymeric material. The composition comprises a continuous phase and a discontinuous phase incorporated therein, wherein the continuous phase comprises a first polymeric material and wherein the discontinuous...... invisible polymer coatings....

  20. Polymers and colloids

    Energy Technology Data Exchange (ETDEWEB)

    Schurtenberger, P. [ETH Zurich, Inst. fuer Polymere, Zurich (Switzerland)


    A wealth of structural information from colloid and polymer solutions on a large range of length scales can be obtained using small angle neutron scattering (SANS) experiments. After a general introduction to the field of soft condensed matter, I shall give a few selected examples on how SANS combined with suitable contrast variation schemes can be used to extract information on the size and conformation of polymer coils in solution and in the melt, and on the local structure and flexibility of polymerlike micelles and microemulsions. (author) 8 figs., tabs., 44 refs.

  1. 'Stuffed' conducting polymers

    DEFF Research Database (Denmark)

    Winther-Jensen, Bjørn; Chen, Jun; West, Keld


    Conducting polymers (CP) obtained by oxidative polymerization using iron(III) salts shrink when Fe(II) and the excess counter ions are washed out after polymerization. This phenomenon can be used to incorporate active molecules into the CP matrix via their addition to the wash liquid. In the pres....... In the present work we demonstrate this principle on three different CP's: polypyrrole (PPy), poly-terthiophene (PTTh) and poly(3,4-ethylenedioxy thiophene) (PEDT), using ferrocene as a model molecule to be trapped in the polymer films. (c) 2005 Elsevier Ltd. All rights reserved....

  2. Nanoparticles from Renewable Polymers

    Directory of Open Access Journals (Sweden)

    Frederik Roman Wurm


    Full Text Available The use of polymers from natural resources can bring many benefits for novel polymeric nanoparticle systems. Such polymers have a variety of beneficial properties such as biodegradability and biocompatibility, they are readily available on large scale and at low cost. As the amount of fossil fuels decrease, their application becomes more interesting even if characterization is in many cases more challenging due to structural complexity, either by broad distribution of their molecular weights polysaccharides, polyesters, lignin or by complex structure (proteins, lignin. This review summarizes different sources and methods for the preparation of biopolymer-based nanoparticle systems for various applications.

  3. Antibacterial polymer coatings.

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Mollye C.; Allen, Ashley N.; Barnhart, Meghan; Tucker, Mark David; Hibbs, Michael R.


    A series of poly(sulfone)s with quaternary ammonium groups and another series with aldehyde groups are synthesized and tested for biocidal activity against vegetative bacteria and spores, respectively. The polymers are sprayed onto substrates as coatings which are then exposed to aqueous suspensions of organisms. The coatings are inherently biocidal and do not release any agents into the environment. The coatings adhere well to both glass and CARC-coated coupons and they exhibit significant biotoxicity. The most effective quaternary ammonium polymers kills 99.9% of both gram negative and gram positive bacteria and the best aldehyde coating kills 81% of the spores on its surface.

  4. Polymer Chemistry in High School. (United States)

    Stucki, Roger


    Discusses why polymer chemistry should be added to the general chemistry curriculum and what topics are appropriate (listing traditional with related polymer topics). Also discusses when and how these topics should be taught. (JN)

  5. Edible Polymers: Challenges and Opportunities

    Directory of Open Access Journals (Sweden)

    Subhas C. Shit


    Full Text Available Edible polymers have established substantial deliberation in modern eons because of their benefits comprising use as edible materials over synthetic polymers. This could contribute to the reduction of environmental contamination. Edible polymers can practically diminish the complexity and thus improve the recyclability of materials, compared to the more traditional non-environmentally friendly materials and may be able to substitute such synthetic polymers. A synthetic hydrogel polymer unlocked a new possibility for development of films, coatings, extrudable pellets, and synthetic nanopolymers, particularly designed for medical, agricultural, and industrial fields. Edible polymers offer many advantages for delivering drugs and tissue engineering. Edible polymer technology helps food industries to make their products more attractive and safe to use. Novel edible materials have been derived from many natural sources that have conventionally been regarded as discarded materials. The objective of this review is to provide a comprehensive introduction to edible polymers by providing descriptions in terms of their origin, properties, and potential uses.

  6. Polymer architecture and drug delivery. (United States)

    Qiu, Li Yan; Bae, You Han


    Polymers occupy a major portion of materials used for controlled release formulations and drug-targeting systems because this class of materials presents seemingly endless diversity in topology and chemistry. This is a crucial advantage over other classes of materials to meet the ever-increasing requirements of new designs of drug delivery formulations. The polymer architecture (topology) describes the shape of a single polymer molecule. Every natural, seminatural, and synthetic polymer falls into one of categorized architectures: linear, graft, branched, cross-linked, block, star-shaped, and dendron/dendrimer topology. Although this topic spans a truly broad area in polymer science, this review introduces polymer architectures along with brief synthetic approaches for pharmaceutical scientists who are not familiar with polymer science, summarizes the characteristic properties of each architecture useful for drug delivery applications, and covers recent advances in drug delivery relevant to polymer architecture.

  7. Conducting polymer 3D microelectrodes

    DEFF Research Database (Denmark)

    Sasso, Luigi; Vazquez, Patricia; Vedarethinam, Indumathi


    Conducting polymer 3D microelectrodes have been fabricated for possible future neurological applications. A combination of micro-fabrication techniques and chemical polymerization methods has been used to create pillar electrodes in polyaniline and polypyrrole. The thin polymer films obtained...... showed uniformity and good adhesion to both horizontal and vertical surfaces. Electrodes in combination with metal/conducting polymer materials have been characterized by cyclic voltammetry and the presence of the conducting polymer film has shown to increase the electrochemical activity when compared...

  8. Shape memory polymer medical device (United States)

    Maitland, Duncan [Pleasant Hill, CA; Benett, William J [Livermore, CA; Bearinger, Jane P [Livermore, CA; Wilson, Thomas S [San Leandro, CA; Small, IV, Ward; Schumann, Daniel L [Concord, CA; Jensen, Wayne A [Livermore, CA; Ortega, Jason M [Pacifica, CA; Marion, III, John E.; Loge, Jeffrey M [Stockton, CA


    A system for removing matter from a conduit. The system includes the steps of passing a transport vehicle and a shape memory polymer material through the conduit, transmitting energy to the shape memory polymer material for moving the shape memory polymer material from a first shape to a second and different shape, and withdrawing the transport vehicle and the shape memory polymer material through the conduit carrying the matter.

  9. Polymers in our daily life

    Directory of Open Access Journals (Sweden)

    Hassan Namazi


    Full Text Available Polymers are widely used advanced materials, which are found almost in every material used in our daily life. To date, the importance of polymers has been much more highlighted because of their applications in different dominions of sciences, technologies and industry – from basic uses to biopolymers and therapeutic polymers. The main aim of this editorial is to accentuate the pragmatic impacts of polymers in human daily life.

  10. Statistical properties of curved polymer

    Indian Academy of Sciences (India)

    For semiflexible polymers, the relevant non-dimensional quantity is lp/L, where lp is the persistence length (which is proportional to the bending modulus k) and L is the contour length of the polymer. In the limit, lp/L ≪ 1, the polymer behaves as a flexible polymer whereas in the limit lp/L ≥ 1 it behaves like a straight rod. For.

  11. Nonlinear microstructured polymer optical fibres

    DEFF Research Database (Denmark)

    Frosz, Michael Henoch

    is potentially the case for microstructured polymer optical fibres (mPOFs). Another advantage is that polymer materials have a higher biocompatibility than silica, meaning that it is easier to bond certain types of biosensor materials to a polymer surface than to silica. As with silica PCFs, it is difficult...

  12. Viscoelastic Properties of Polymer Blends (United States)

    Hong, S. D.; Moacanin, J.; Soong, D.


    Viscosity, shear modulus and other viscoelastic properties of multicomponent polymer blends are predicted from behavior of individual components, using a mathematical model. Model is extension of two-component-blend model based on Rouse-Bueche-Zimm theory of polymer viscoelasticity. Extension assumes that probabilities of forming various possible intracomponent and intercomponent entanglements among polymer molecules are proportional to relative abundances of components.

  13. White polymer light-emitting diode based on polymer blending

    International Nuclear Information System (INIS)

    Lee, Yong Kyun; Kwon, Soon Kab; Kim, Jun Young; Park, Tae Jin; Song, Dae Ho; Kwon, Jang Hyuk; Choo, Dong Jun; Jang, Jin; Jin, Jae Kyu; You, Hong


    A series of white polymer light emitting devices have been fabricated by using a polymer blending system of polyfluorene-based blue and MEH-PPV red polymers. A device structure of ITO/PEDOT:PSS/polymer/LiF/Al was employed. The white polymer device exhibited a current efficiency of 4.33 cd/A (4,816 cd/m 2 , Q.E. = 1.9 %) and a maximum luminance of 21,430 cd/m 2 at 9.2 V. The CIE coordinates were (0.35, 0.37) at 5 V and (0.29, 0.30) at 9 V.

  14. based gel polymer electrolytes

    Indian Academy of Sciences (India)

    Bull. Mater. Sci., Vol. 29, No. 7, December 2006, pp. 673–678. © Indian Academy of Sciences. 673. Investigation on poly (vinylidene fluoride) based gel polymer electrolytes ... (Alamgir and Abraham 1993; Sukeshini et al 1996; Ra- jendran and Uma ... Yang et al 1996; Ramesh and Arof 2001) and such elec- trolytes exhibit ...

  15. Raw and renewable polymers

    CSIR Research Space (South Africa)

    Joseph, S


    Full Text Available with enhanced support for global sustainability. High performance plastics are the outcome of continuous research over the last few decades. The real challenge of renewable polymers lies in finding applications, which will result in mass production, and price...

  16. Knots in polymers

    Indian Academy of Sciences (India)

    Knots and topological entanglements play an important role in the statistical mechanics of polymers. While topological entanglement is a global property, it is possible to study the size of a knotted region both numerically and analytically. It can be shown that long-range repulsive interactions, as well as entropy favor small ...

  17. Conformational properties of polymers

    Indian Academy of Sciences (India)

    Abstract. We discuss exact enumeration technique and its application to polymers and biopolymers. Using this method one can obtain phase diagram in thermodynamic limit. The method works quite well in describing the outcomes of single molecule force spectroscopy results where finite size effects play a crucial role.

  18. Polymers of phenylenediamines

    Czech Academy of Sciences Publication Activity Database

    Stejskal, Jaroslav


    Roč. 41, February (2015), s. 1-31 ISSN 0079-6700 R&D Projects: GA ČR(CZ) GA13-00270S Institutional support: RVO:61389013 Keywords : polyphenylenediamine * phenylenediamine * conducting polymers Subject RIV: CD - Macromolecular Chemistry Impact factor: 27.184, year: 2015

  19. Polyester polymer concrete overlay. (United States)


    Polyester polymer concrete (PPC) was used in a trial application on a section of pavement that suffers from extensive studded tire wear. The purpose of the trial section is to determine if PPC is a possible repair strategy for this type of pavement d...

  20. Pulsed lasers versus continuous light sources in capillary electrophoresis and fluorescence detection studies: Photodegradation pathways and models

    Energy Technology Data Exchange (ETDEWEB)

    Boutonnet, Audrey; Morin, Arnaud [Picometrics Technologies, 478 Rue de la Découverte, Labège France (France); Petit, Pierre [Institut de Mathématiques, Université de Toulouse, Université Paul Sabatier, Toulouse CEDEX 04 (France); Vicendo, Patricia; Poinsot, Véréna [Laboratoire des IMRCP, UMR 5623, Université de Toulouse, Université Paul Sabatier, Toulouse CEDEX 04 (France); Couderc, François, E-mail: [Laboratoire des IMRCP, UMR 5623, Université de Toulouse, Université Paul Sabatier, Toulouse CEDEX 04 (France)


    Pulsed lasers are widely used in capillary electrophoresis (CE) studies to provide laser induced fluorescence (LIF) detection. Unfortunately pulsed lasers do not give linear calibration curves over a wide range of concentrations. While this does not prevent their use in CE/LIF studies, the non-linear behavior must be understood. Using 7-hydroxycoumarin (7-HC) (10–5000 nM), Tamra (10–5000 nM) and tryptophan (1–200 μM) as dyes, we observe that continuous lasers and LEDs result in linear calibration curves, while pulsed lasers give polynomial ones. The effect is seen with both visible light (530 nm) and with UV light (355 nm, 266 nm). In this work we point out the formation of byproducts induced by pulsed laser upon irradiation of 7-HC. Their separation by CE using two Zeta LIF detectors clearly shows that this process is related to the first laser detection. All of these photodegradation products can be identified by an ESI-/MS investigation and correspond to at least two 7HC dimers. By using the photodegradation model proposed by Heywood and Farnsworth (2010) and by taking into account the 7-HC results and the fact that in our system we do not have a constant concentration of fluorophore, it is possible to propose a new photochemical model of fluorescence in LIF detection. The model, like the experiment, shows that it is difficult to obtain linear quantitation curves with pulsed lasers while UV-LEDs used in continuous mode have this advantage. They are a good alternative to UV pulsed lasers. An application involving the separation and linear quantification of oligosaccharides labeled with 2-aminobezoic acid is presented using HILIC and LED (365 nm) induced fluorescence. - Highlights: • No linear calibration curves are obtained in CE/Pulsed-LIF detection. • Photodegradation and photodimerisation are responsible of this non linearity. • A mathematical model of this phenomenon is presented. • 7 hydroxycoumarin in CE/LIF is used to verify the

  1. Surface tension of polymer melts - experimental investigations of its effect on polymer-polymer adhesion

    DEFF Research Database (Denmark)

    Jankova Atanasova, Katja; Islam, Mohammad Aminul; Hansen, Hans Nørgaard

    -polymer bond strength during two component polymer processing. Polymer materials PS, POM, ABS, PEl, PEEK and PC are chosen for the investigation. Pendant drop method showed that in case of PS and POM, the melt surface tension was decreased with increasing temperature. The substrate surface energies...

  2. Surface tension of polymer melts - experimental investigations of its effects on polymer-polymer adhesion

    DEFF Research Database (Denmark)

    Islam, Mohammad Aminul; Jankova Atanasova, Katja; Hansen, Hans Nørgaard

    -polymer bond strength during two component polymer processing. Polymer materials PS, POM, ABS, PEI, PEEK and PC are chosen for the investigation. Pendant drop method showed that in case of PS and POM, the melt surface tension was decreased with increasing temperature. The substrate surface energies...

  3. Gel polymer electrolytes for batteries (United States)

    Balsara, Nitash Pervez; Eitouni, Hany Basam; Gur, Ilan; Singh, Mohit; Hudson, William


    Nanostructured gel polymer electrolytes that have both high ionic conductivity and high mechanical strength are disclosed. The electrolytes have at least two domains--one domain contains an ionically-conductive gel polymer and the other domain contains a rigid polymer that provides structure for the electrolyte. The domains are formed by block copolymers. The first block provides a polymer matrix that may or may not be conductive on by itself, but that can soak up a liquid electrolyte, thereby making a gel. An exemplary nanostructured gel polymer electrolyte has an ionic conductivity of at least 1.times.10.sup.-4 S cm.sup.-1 at C.

  4. Frictional properties of confined polymers

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N; Persson, Bo N J


    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force...

  5. Conducting Polymers for Neutron Detection

    International Nuclear Information System (INIS)

    Clare Kimblin; Kirk Miller; Bob Vogel; Bill Quam; Harry McHugh; Glen Anthony; Steve Jones; Mike Grover


    Conjugated polymers have emerged as an attractive technology for large-area electronic applications. As organic semiconductors, they can be used to make large-area arrays of diodes or transistors using fabrication techniques developed for polymer coatings, such as spraying and screen-printing. We have demonstrated both neutron and alpha detection using diodes made from conjugated polymers and have done preliminary work to integrate a boron carbide layer into the conventional polymer device structure to capture thermal neutrons. The polymer devices appear to be insensitive to gamma rays, due to their small physical thickness and low atomic number

  6. Conducting Polymers for Neutron Detection

    Energy Technology Data Exchange (ETDEWEB)

    Kimblin, Clare; Miller, Kirk; Vogel, Bob; Quam, Bill; McHugh, Harry; Anthony, Glen; Mike, Grover


    Conjugated polymers have emerged as an attractive technology for large-area electronic applications. As organic semiconductors, they can be used to make large-area arrays of diodes or transistors using fabrication techniques developed for polymer coatings, such as spraying and screen-printing. We have demonstrated both neutron and alpha detection using diodes made from conjugated polymers and have done preliminary work to integrate a boron carbide layer into the conventional polymer device structure to capture thermal neutrons. The polymer devices appear to be insensitive to gamma rays, due to their small physical thickness and low atomic number.

  7. Enhancement of catalytic, reusability, and long-term stability features of Trametes versicolor IBL-04 laccase immobilized on different polymers. (United States)

    Asgher, Muhammad; Noreen, Sadia; Bilal, Muhammad


    In the current study, different bio-polymers such as agar-agar, polyacrylamide and gelatin were utilized as bolster materials for the immobilization of a fungal laccase through entrapment approach. Among the polymers, agar-agar matrix most firmly encapsulated the enzyme yielding significant laccase immobilization (79.65±2.55%). Immobilization prolonged the reaction time of laccase and agar-agar, polyacrylamide and gelatin entrapped laccases displayed maximum catalytic activities after 10.0, 15.0 and 10.0min of reaction, respectively, as compared to free counterpart (5.0min). It also increased the optimal temperature by 5.0-10°C and provided an alkaline shift of the pH optima to agar-agar and gelatin entrapped laccase, while, in case of polyacrylamide, optimum pH was displaced to acidic region. Kinetic data revealed that K m(app) values were slightly increased while V max values were decreased as compared to free counterpart. Polymers encapsulation led to significant improvement in activity against thermal denaturation. After 180min at 60°C, the enzymes preserved 28.1±0.9, 48.6±1.3 and 32.5±1.8% residual activities, respectively, whereas, the free enzyme was completely inactive. Immobilization enabled the enzymes to resist a number of different effectors including metal ions, inhibitors/denaturants and chelating agents. Moreover, the resulted modified laccases displayed good recycling capability for substrate-oxidation reactions in several successive batches. In summary, the tremendously improved attributes of polymers-encapsulated enzymes display a high potential for various applications in different industrial sectors. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Dissolving Polymers in Ionic Liquids. (United States)

    Hoagland, David; Harner, John


    Dissolution and phase behavior of polymers in ionic liquids have been assessed by solution characterization techniques such as intrinsic viscosity and light scattering (static and dynamic). Elevated viscosity proved the greatest obstacle. As yet, whether principles standard to conventional polymer solutions apply to ionic liquid solutions is uncertain, especially for polymers such as polyelectrolytes and hydrophilic block copolymers that may specifically interact with ionic liquid anions or cations. For flexible polyelectrolytes (polymers releasing counterions into high dielectric solvents), characterization in ionic liquids suggests behaviors more typical of neutral polymer. Coil sizes and conformations are approximately the same as in aqueous buffer. Further, several globular proteins dissolve in a hydrophilic ionic liquid with conformations analogous to those in buffer. General principles of solubility, however, remain unclear, making predictions of which polymer dissolves in which ionic liquid difficult; several otherwise intractable polymers (e.g., cellulose, polyvinyl alcohol) dissolve and can be efficiently functionalized in ionic liquids.

  9. Adsorption and flocculation by polymers and polymer mixtures. (United States)

    Gregory, John; Barany, Sandor


    Polymers of various types are in widespread use as flocculants in several industries. In most cases, polymer adsorption is an essential prerequisite for flocculation and kinetic aspects are very important. The rates of polymer adsorption and of re-conformation (relaxation) of adsorbed chains are key factors that influence the performance of flocculants and their mode of action. Polyelectrolytes often tend to adopt a rather flat adsorbed configuration and in this state their action is mainly through charge effects, including 'electrostatic patch' attraction. When the relaxation rate is quite low, particle collisions may occur while the adsorbed chains are still in an extended state and flocculation by polymer bridging may occur. These effects are now well understood and supported by much experimental evidence. In recent years there has been considerable interest in the use of multi-component flocculants, especially dual-polymer systems. In the latter case, there can be significant advantages over the use of single polymers. Despite some complications, there is a broad understanding of the action of dual polymer systems. In many cases the sequence of addition of the polymers is important and the pre-adsorbed polymer can have two important effects: providing adsorption sites for the second polymer or causing a more extended adsorbed conformation as a result of 'site blocking'. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. In-capillary enrichment, proteolysis and separation using capillary electrophoresis with discontinuous buffers: application on proteins with moderately acidic and basic isoelectric points. (United States)

    Nesbitt, Chandra A; Yeung, Ken K-C


    Advances in mass spectrometry and capillary-format separation continue to improve the sensitivity of protein analysis. Of equal importance is the miniaturization of sample pretreatment such as enrichment and proteolysis. In a previous report (Nesbitt et al., Electrophoresis, 2008, 29, 466-474), nanoliter-volume protein enrichment, tryptic digestion, and partial separation was demonstrated in capillary electrophoresis followed by MALDI mass spectral analysis. A discontinuous buffer system, consisting of ammonium (pH 10) and acetate (pH 4), was used to create a pH junction inside the capillary, trapping a protein with a neutral isoelectric point, myoglobin (pI 7.2). Moreover, co-enrichment of myoglobin with trypsin led to an in-capillary digestion. In this paper, the ability of this discontinuous buffer system to perform similar in-capillary sample pretreatment on proteins with moderately acidic and basic pI was studied and reported. Lentil lectin (pI 8.6) and a multi-phosphorylated protein, beta-casein (pI 5.1), were selected as model proteins. In addition to the previously shown tryptic digestion, proteolysis with endoproteinase Asp-N was also performed. Digestion of these acidic and basic pI proteins produced a few peptides with extreme pI values lying outside the trapping range of the discontinuous buffer. An alteration in the peptide trapping procedure was made to accommodate these analytes. Offline MALDI mass spectral analysis confirmed the presence of the expected peptides. The presented miniaturized sample pretreatment methodology was proven to be applicable on proteins with a moderately wide range of pI. Flexibility in the choice of protease was also evident.

  11. Laser-assisted welding of transparent polymers for microchemical engineering and life science (United States)

    Pfleging, Wilhelm; Baldus, Oliver; Bruns, M.; Baldini, Alessandro; Bemporad, Edoardo


    In this contribution experimental studies on the laser-assisted welding of transparent polymers with diode laser (wavelength 940 nm) are presented to discuss their potential for the fabrication of micro-devices for micro-chemical engineering and life science. Micro-channel devices such as capillary electrophoresis chips, heat exchangers or static mixers for liquids and gases consist of different micro-patterned sheets with structural details in the range of a few μm. In micro-chemical engineering, in general the sheets of micro-devices are made of metals. In our approaches the use of transparent and micro-patterned polymers such as polyvinylidene fluoride (PVDF) is investigated. For the development of micro-devices in life science the use of sheets made of transparent polymers such as polymethylmethacrylate (PMMA) is presented, e.g., in capillary electrophoresis chips. Devices are built up by stacks of micro-patterned sheets which have to be joined. These sheets are patterned by micro-milling, CO2-laser cutting or hot embossing. Laser-assisted polymer welding of transparent and opaque materials is well established. But the welding of only transparent components is still a challenge in micro-system technology, especially if micro-structures are included. For this purpose very thin absorbing layers with a thickness of about 5nm to 20nm are used in order to establish a welding process between transparent and micro-patterned polymers. The strength of the bonding is characterized by tensile tests as function of absorbing layer thickness, temperature, laser scan velocity and laser scan overlap. The topography is investigated with atomic force microscopy and low voltage scanning electron microscopy.

  12. Controlled slow release of anticancer drugs from protein-hydrophilic vinyl polymer carriers

    International Nuclear Information System (INIS)

    Asano, Masaharu; Yoshida, Masaru; Kaetsu, Isao


    The release behavior has been studied for bleomycin hydrochloride (BLM), an anticancer drug, from carrier composities prepared from mixtures of proteins and hydrophilic vinyl monomers by combined procedures of radiation polymerization and thermal denaturation. The magnitude, Q/tsup(1/2), for BLM release was the smallest when albumin was denatured by thermal treatment after the polymerization of albumin-2-hydroxyethyl methacrylate (HEMA) by radiation at -78 0 C. This retardation was further enhanced by the use of cross-linked polymers. On the other hand, the digestion of the albumin-HEMA composite, during the release test carried out in the saline containing some proteases, was markedly suppressed with increasing the HEMA content in the composite. The digestion was lowered more than expected from the albumin content in the composite. In summary of the release tests and the scanning electron microscopic observations, it was concluded that the release of BLM and the digestion of albumin component contained in the composites can be markedly suppressed by the incorporation of the polymeric component. (author)

  13. Dynamic and structural study of neocarzinostatin native and denatured states, by differential microcalorimetry, optical spectroscopies and X-ray and neutron scattering

    International Nuclear Information System (INIS)

    Russo, Daniela


    A structural and dynamic characterization of proteins denatured states is essential to the understanding of mechanisms which control proteins folding. It is in this framework that this study has been undertaken in taking as model the neocarzinostatin globular protein. It is formed with seven cell-layers which form a barrel pattern maintained by two bi-sulfur bonds. A full characterization of native and denatured states, both from structural and dynamic point of view, has been implemented with several techniques able to bring data at different levels. During the experiments, ncs has been stabilized by temperature and by the use of a chaotropic agent: the guanidinium chloride (gdmcl). Small angle x-ray and neutron scattering have allowed us to obtain data on the variation of the protein compactness in terms of gdmcl temperature and concentration. The diffusion spectra show that ncs loses completely its globular structure above 80 C or in presence of about 5 m of gdmcl. Temperature and concentration of half denaturation are tm= 70 C and cm=3.5 m (in heavy water), respectively. Spectra analysis of strongly denatured protein has allowed us to obtain values of its chain length and of its persistence length which are in agreement with those theoretically estimated. Experiments have been carried out too to measure the radius of gyration to zero concentration and the second virial coefficient of the solution in order to estimate the interactions between the molecules. A full characterization has been performed in terms of gdmcl temperature and concentration by fluorescence and circular dichroism. These two techniques reveal the variations of the local three-dimensional structure and secondary structure of the protein respectively. Microcalorimetry measurements have shown that thermal denaturation of ncs is completely reversible and has been used to measure the enthalpy variation during the transition. At last, it has been possible to study ncs intramolecular dynamics in

  14. Denatured Whey Protein Powder as a New Matrix Excipient: Design and Evaluation of Mucoadhesive Tablets for Sustained Drug Release Applications. (United States)

    Hsein, Hassana; Garrait, Ghislain; Tamani, Fahima; Beyssac, Eric; Hoffart, Valérie


    In earlier study, we proposed denatured whey protein (DWP) powder obtained by atomization as a new excipient to promote oral drug delivery. In this work, we evaluate the possibility to formulate tablets based on DWP powders and to characterize their role as a matrix mucoadhesive excipient. Tablets containing increased amount of DWP (10 to 30%) were produced by direct compression after mixing with theophylline, microcrystalline cellulose, Aerosil® and magnesium stearate. Dissolution behaviors of obtained tablets were evaluated in different USP buffers (pH 1.2, 4.5 and 6.8) and in simulated gastric and intestinal fluids and mechanisms analyzed by multiple mathematical models. Swelling, erosion and mucoadhesion were also evaluated. Finally, release and absorption were studied in the artificial digestive system (TIM 1). Tablets based on DWP and containing 300 mg of theophylline were obtained by direct compression. These tablets exhibited controlled release driven by diffusion starting from 15% DWP content whatever the pH studied. They also showed a great extent of swelling and water uptake while matrix weight loss was limited. Addition of enzymes accelerated drug release which became governed by erosion according to Peppas model. The present study shows that DWP powders can be successfully used as a pharmaceutical excipient, and in particular as a matrix mucoadhesive controlled release tablets.

  15. Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis (United States)

    Lopez, Isabel; Ruiz-Larrea, Fernanda; Cocolin, Luca; Orr, Erica; Phister, Trevor; Marshall, Megan; VanderGheynst, Jean; Mills, David A.


    Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria. PMID:14602643

  16. Profiling of a microbial community under confined conditions in a fed-batch garbage decomposer by denaturing gradient gel electrophoresis. (United States)

    Horisawa, Sakae; Sakuma, Yoh; Nakamura, Yasunori; Doi, Shuichi


    In order to determine the conditions for the maximum performance of a fed-batch composting (FBC) reactor, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the microbial communities established under the confined conditions of moisture content and environmental temperature. To evaluate the effects of microbial community structures on the performance of FBC reactors, degradation experiments using small-scale reactors and model waste were conducted under confined environmental conditions. A high degradation rate was observed under a wide range of MC conditions (30-60%) and at higher than usual temperatures (30-50 degrees C). The microbial communities that formed in the experimental FBC reactors were analyzed by DGGE of PCR-amplified 16S rRNA genes. The DGGE banding patterns at the same level as the degradation rates were similar even if the environmental conditions were different. Sequence analysis of the DGGE bands revealed the primary microbes which act in the reactor.

  17. Analysis of sequence homogenisation in rDNA arrays of Haemonchus contortus by denaturing gradient gel electrophoresis. (United States)

    Gasser, R B; Zhu, X; Chilton, N B; Newton, L A; Nedergaard, T; Guldberg, P


    Testing different theories of concerted evolution experimentally has been hampered mainly due to the lack of appropriate model systems and technical limitations. In this study, we employed a denaturing gradient gel electrophoresis (DGGE) approach for the display and definition of nucleotide variations in the second internal transcribed spacer (ITS-2) of ribosomal DNA (rDNA) of the parasitic nematode, Haemonchus contortus. The ITS-2 was amplified from individual adult nematodes by PCR and subjected to DGGE. Of the 94 individuals (representing nine different populations) analysed, 13 different DGGE profiles were displayed. Eighteen bands representing those profiles were excised and sequenced. Sequencing defined 13 different types of ITS-2 with 12 nucleotide variations (4 transitions, 5 transversions, 1 insertion and 2 deletions) which could be related to particular positions of the predicted secondary structure for the ITS-2 pre-rRNA. The results showed that individuals of interbreeding populations of H. contortus can have rDNA arrays that are partially or fully homogenised for different sequence variants (despite interindividual variation), suggesting that the homogenisation process is driven mainly by intrachromosomal exchange. The findings also demonstrated the capacity of the DGGE-sequencing strategy to quantify the frequency of ITS-2 sequence types within individual nematodes from different populations without the need for cloning or Southern blot procedures. This has important implications for studying the mechanisms of sequence homogenisation in rDNA and pre-rRNA processing as well as for elucidating speciation events and population differentiation at the molecular level.

  18. Microbial Diversity during Fermentation of Sweet Paste, a Chinese Traditional Seasoning, Using PCR-Denaturing Gradient Gel Electrophoresis. (United States)

    Mao, Ping; Hu, Yuanliang; Liao, Tingting; Wang, Zhaoting; Zhao, Shumiao; Liang, Yunxiang; Hu, Yongmei


    The aim of this study was to elucidate the changes in the microbial community and biochemical properties of a traditional sweet paste during fermentation. PCR-denaturing gradient gel electrophoresis (DGGE) analysis showed that Aspergillus oryzae was the predominant species in the koji (the fungal mixture), and the majority of the fungi isolated belonged to two Zygosaccharomyces species in the mash. The bacterial DGGE profiles revealed the presence of Bacillus subtilis during fermentation, and Lactobacillus acidipiscis, Lactobacillus pubuzihii, Lactobacillus sp., Staphylococcus kloosi, and several uncultured bacteria were also detected in the mash after 14 days of main fermentation. Additionally, during main fermentation, amino-type nitrogen and total acid increased gradually to a maximum of 6.77 ± 0.25 g/kg and 19.10 ± 0.58 g/kg (30 days) respectively, and the concentration of reducing sugar increased to 337.41 ± 3.99 g/kg (7 days). The 180-day fermented sweet paste contained 261.46 ± 19.49 g/kg reducing sugar and its pH value remained at around 4.65. This study has used the PCR-DGGE technique to demonstrate the microbial community (including bacteria and fungi) in sweet paste and provides useful information (biochemical properties) about the assessment of the quality of sweet paste throughout fermentation.

  19. Cowpea Vicilins: Fractionation of Urea Denatured Sub-Units and Effects on Callosobruchus maculatus F. (Coleoptera: Bruchidae Development

    Directory of Open Access Journals (Sweden)

    Antônio Chagas Mota


    Full Text Available Vicilins (7S storage globulins isolated from cowpea (Vigna unguiculata L. seeds which were susceptible (S and resistant (R to the cowpea weevil (Callosobruchus maculatus F., Coleoptera: Bruchidae were denatured by urea and fractionated by ion-exchange chromatography. Isolated fractions were incorporated in artificial seeds for assessment of their toxicity to C. maculatus. The most acidic fractions of both susceptible (CE-31 cultivar and resistant (IT81D-1045 line seeds were shown to affect development and survival of the bruchid. Results indicated that vicilin polypeptides of toxic nature were expressed in both types of storage globulins although at different levels.Vicilinas (globulinas de reserva 7S isoladas de sementes de feijão-de-corda (Vigna unguiculata L., susceptíveis (S e resistentes (R ao caruncho/gorgulho (Callosobruchus maculatus F., Coleoptera: Bruchidae foram desnaturadas por uréia e fracionadas por cromatografia de troca iônica. As frações isoladas foram incorporadas em sementes artificiais para avaliação de sua toxicidade a C. maculatus. As fracões mais ácidas de ambas vicilinas afetaram o desenvolvimento e a sobrevivência do bruquídeo. Sugerimos que polipeptídeos de vicilinas de natureza tóxica são expressos em ambos tipos de globulinas de reserva, embora em níveis diferentes.

  20. Variations among Japanese of the factor IX gene (F9) detected by PCR-denaturing gradient gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Satoh, Chiyoko; Takahashi, Norio; Asakawa, Junichi; Hiyama, Keiko; Kodaira, Meiko (Radiation Effects Research Foundation, Hiroshima (Japan))


    In the course of feasibility studies to examine the efficiencies and practicalities of various techniques for screening for genetic variations, the human coagulation factor IX (F9) genes of 63 Japanese families were examined by PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Four target sequences with lengths of 983-2,891 bp from the F9 genes of 126 unrelated individuals from Hiroshima and their 100 children were amplified by PCR, digested with restriction enzymes to approximately 500-bp fragments, and examined by DGGE - a total of 6,724 bp being examined per individual. GC-rich sequences (GC-clamps) of 40 bp were attached to both ends of the target sequences, as far as was feasible. Eleven types of new nucleotide substitutions were detected in the population, none of which produced RFLPs or caused hemophilia B. By examining two target sequences in a single lane, approximately 8,000 bp in a diploid individual could be examined. This approach is very effective for the detection of variations in DNA and is applicable to large-scale population studies. 46 refs., 3 figs., 1 tab.

  1. Analysis of microbial diversity on deli slicers using polymerase chain reaction and denaturing gradient gel electrophoresis technologies. (United States)

    Koo, O K; Mertz, A W; Akins, E L; Sirsat, S A; Neal, J A; Morawicki, R; Crandall, P G; Ricke, S C


    Cross-contamination of pathogenic and spoilage bacteria from food-contact surfaces to food products is a serious public health issue. Bacteria may survive and attach to food-contact surfaces by residual food components and/or background bacteria which may subsequently transfer to other food products. Deli slicers, generally used for slicing ready-to-eat products, can serve as potential sources for considerable bacterial transfer. The objective of this study was to assess the extent and distribution of microbial diversity of deli slicers by identification of pathogenic and background bacteria. Slicer-swab samples were collected from restaurants in Arkansas and Texas in the United States. Ten surface areas for each slicer were swabbed using sterile sponges. Denaturing gradient gel electrophoresis (DGGE) was applied to investigate the fingerprint of samples, and each band was further identified by sequence analysis. Pseudomonads were identified as the dominant bacteria followed by Enterobacteriaceae family, and lactic acid bacteria such as Lactococcus lactis and Streptococcus thermophilus were also found. Bacterial distribution was similar for all surface areas, while the blade guard exhibited the greatest diversity. This study provides a profile of the microbial ecology of slicers using DGGE to develop more specific sanitation practices and to reduce cross-contamination during slicing. © 2012 The Society for Applied Microbiology.

  2. Enhancing recombinant interleukin-6 production yield by fermentation optimization, two-step denaturing, and one-step purification. (United States)

    Ahmed, Nadeem; Abbas, Rabbia; Khan, Mohsin Ahmad; Bashir, Hamid; Tahir, Saad; Zafar, Ahmad Usman


    Interleukin-6 a pleiotropic cytokine involved in a wide range of biological activities. So the large-scale production of biologically active recombinant human interleukin-6 is important for its structural and functional studies. Here, we report an optimized method for shake flask fermentation and a simplified high-yield purification procedure for the recombinant interleukin-6. This high-yield expression method not only involves the optimization of the fermentation condition but also the single step purification method as well as a two-step denaturing and one-step refolding process. This approach replaces the more conventional procedure of protein solubilization and refolding. Through applying these strategies, the final cell density and overall product yield of the recombinant human interleukin-6 were obtained as 20.4 g as cell biomass and 150 mg as purified active protein from the I-L of the culture. The purified protein was characterized by HPLC and SDS-PAGE. The results of the current work demonstrate that the described method may be used to develop the process for industrial-scale production of the biologically active recombinant interleukin-6 protein. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

  3. Denaturing gradient gel electrophoresis (DGGE as a powerful novel alternative for differentiation of epizootic ISA virus variants.

    Directory of Open Access Journals (Sweden)

    Marisela Carmona

    Full Text Available Infectious Salmon Anemia is a devastating disease critically affecting world-wide salmon production. Chile has been particularly stricken by this disease which in all cases has been directly related with its causative agent, a novel orthomyxovirus which presents specific and distinctive infective features. Among these, two molecular markers have been directly associated with pathogenicity in two of the eight RNA sub genomic coding units of the virus: an insertion hot spot region present in viral segment 5 and a Highly Polymorphic Region (HPR located in viral segment 6. Here we report the successful adaptation of a PCR-dependent denaturing gel electrophoresis technique (DGGE, which enables differentiation of selected reported HPR epizootic variants detected in Chile. At the same time, the technique allows us to distinguish one nucleotide differences in sequences associated with the intriguing, and still not well-understood, insertion events which tend to occur on RNA Segment 5. Thus, the versatility of the technique opens new opportunities for improved understanding of the complex biology of all ISA variants as well as possible applications to other highly variable pathogens.

  4. Detection of bacteria in normal adult nasal cavity based on polymerase chain reaction-denaturing gradient gel electrophoresis. (United States)

    Cho, Jae Hoon; Jung, Min Young; Kim, Jin Kook; Chang, Young-Hyo


    This study investigated the bacterial diversity in a normal adult nasal cavity using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S ribosomal RNA (rRNA) gene fragments and compared the results with those of a culture-based method. We swabbed the inferior turbinate from 19 normal volunteers. The transport media was divided by two, one for bacterial culture and another direct extraction for bacterial DNA. PCR-DGGE was performed from the bacterial DNA and all of the sequences were compared with the reference organism by using the BLAST program (a genome database of GenBank in the National Center for Biotechnology Information, Bethesda, MD). All 224 colonies were obtained from 19 samples by using a culture-based method; however, only 9 kinds of bacteria were detected. Staphylococcus epidermidis was the most frequently detected bacteria, and Staphylococcus aureus was the second most. The detection rates of other bacteria were very low. On the other hand, the PCR-DGGE from direct DNA extraction revealed 34 different bands that corresponded to 23 different kinds of bacteria. There were nine genera, viz., Staphylococcus, Bacillus, Enterobacter, Corynebacterium, Actinobacterium, Hafnia, Moraxella, Dolosigranulum, and Clostridium. Among them, unspecific Staphylococcus species and Enterobacter aerogenes were detected most frequently. Compared with the previous culture-based method, PCR-DGGE can detect much more diversity of bacteria in the nasal cavity.

  5. Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity (United States)

    Gu, Zonglin; Yang, Zaixing; Kang, Seung-Gu; Yang, Jerry R.; Luo, Judong; Zhou, Ruhong


    MoS2 nanosheet, a new two-dimensional transition metal dichalcogenides nanomaterial, has attracted significant attentions lately due to many potential promising biomedical applications. Meanwhile, there is also a growing concern on its biocompatibility, with little known on its interactions with various biomolecules such as proteins. In this study, we use all-atom molecular dynamics simulations to investigate the interaction of a MoS2 nanosheet with Villin Headpiece (HP35), a model protein widely used in protein folding studies. We find that MoS2 exhibits robust denaturing capability to HP35, with its secondary structures severely destroyed within hundreds of nanosecond simulations. Both aromatic and basic residues are critical for the protein anchoring onto MoS2 surface, which then triggers the successive protein unfolding process. The main driving force behind the adsorption process is the dispersion interaction between protein and MoS2 monolayer. Moreover, water molecules at the interface between some key hydrophobic residues (e.g. Trp-64) and MoS2 surface also help to accelerate the process driven by nanoscale drying, which provides a strong hydrophobic force. These findings might have shed new light on the potential nanotoxicity of MoS2 to proteins with atomic details, which should be helpful in guiding future biomedical applications of MoS2 with its nanotoxicity mitigated.

  6. Heat-denaturation and aggregation of quinoa (Chenopodium quinoa) globulins as affected by the pH value. (United States)

    Mäkinen, Outi E; Zannini, Emanuele; Koehler, Peter; Arendt, Elke K


    The influence of heating (100 °C; 0-15 min) on the relative molecular mass, protein unfolding and secondary structure of quinoa globulins was studied at pH 6.5 (low solubility), 8.5 and 10.5 (high solubility). The patterns of denaturation and aggregation varied with pH. Heating triggered the disruption of the disulfide bonds connecting the acidic and basic chains of the chenopodin subunits at pH 8.5 and 10.5, but not at pH 6.5. Large aggregates unable to enter a 4% SDS-PAGE gel were formed at pH 6.5 and 8.5, which became soluble under reducing conditions. Heating at pH 10.5 lead to a rapid dissociation of the native chenopodin and to the disruption of the subunits, but no SDS-insoluble aggregates were formed. No major changes in secondary structure occurred during a 15 min heating, but an increase in hydrophobicity indicated unfolding of the tertiary structure in all samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Detection and differentiation of Entamoeba histolytica and Entamoeba dispar in clinical samples through PCR-denaturing gradient gel electrophoresis. (United States)

    López-López, P; Martínez-López, M C; Boldo-León, X M; Hernández-Díaz, Y; González-Castro, T B; Tovilla-Zárate, C A; Luna-Arias, J P


    Amebiasis is one of the twenty major causes of disease in Mexico; however, the diagnosis is difficult due to limitations of conventional microscopy-based techniques. In this study, we analyzed stool samples using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) to differentiate between Entamoeba histolytica (pathogenic) and E. dispar (non-pathogenic). The target for the PCR amplification was a small region (228 bp) of the adh112 gene selected to increase the sensitivity of the test. The study involved 62 stool samples that were collected from individuals with complaints of gastrointestinal discomfort. Of the 62 samples, 10 (16.1%) were positive for E. histolytica while 52 (83.9%) were negative. No sample was positive for E. dispar. These results were validated by nested PCR-RFLP (restriction fragment length polymorphism) and suggest that PCR-DGGE is a promising tool to differentiate among Entamoeba infections, contributing to determine the specific treatment for patients infected with E. histolytica, and therefore, avoiding unnecessary treatment of patients infected with the non-pathogenic E. dispar.

  8. Enrichment of serum low-molecular-weight proteins using C18 absorbent under urea/dithiothreitol denatured environment. (United States)

    Wu, Jing; An, Yuan; Pu, Hai; Shan, Yue; Ren, Xiaoqing; An, Mingrui; Wang, Qingsong; Wei, Shicheng; Ji, Jianguo


    Serum low-molecular-weight proteins (LMWPs, molecular weightbody physiological and pathological situations, whereas many difficulties are encountered when enriching and fractionating them. Using C(18) absorbent (100 A) enrichment and fractionation under urea/dithiothreitol (DTT) denatured environment followed by 60% acetonitrile (ACN) elution, serum LMWPs could be enriched more than 100-fold and were evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis (2-DE), and isotope-coded affinity tag (ICAT) labeling quantification. Proteins existing in human serum at low nanograms/milliliter (ng/ml) levels, such as myeloid-related proteins (MRPs), could be identified directly from 2-DE coupled with matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS) and LTQ-Orbitrap MS. Sixteen proteins were confidentially identified and quantified using ICAT labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS). By virtue of its easy operation and high reproducibility to process large quantity complex serum samples, this method has potential uses in enriching LMWPs either in serum or in cell and tissue samples. Copyright 2009 Elsevier Inc. All rights reserved.

  9. Lactic acid bacteria dynamics during spontaneous fermentation of cocoa beans verified by culture-independent denaturing gradient gel electrophoresis. (United States)

    Santos, T F; Santana, L K A; Santos, A C F; Silva, G S; Romano, C C; Dias, J C T; Rezende, R P


    Cocoa is naturally fermented in the field before the cocoa seeds are removed for processing. We assessed the dynamics of lactic acid bacteria during cocoa fermentation in Bahia, Brazil. During five days of fermentation, temperature and pH were measured and beans were collected for genomic DNA extraction every 12 h. The DNA was used as a template for amplification with Lac1-Lac2 and Lac3-Lac2 for denaturing gradient gel electrophoresis analyses. pH values ranged from 3.34 to 4.98, while the temperature varied from 23° to 50°C. Lac1-Lac2 primers permitted detection of 11 operational taxonomic units. Twenty-eight operational taxonomic units were obtained with the primer pair Lac3-Lac2. It was observed that there were variations between the numbers of operational taxonomic units throughout the process, probably because of changes in pH and temperature. The greatest similarity in amplified samples was obtained with the primers Lac3-Lac2.

  10. [Detection of streptomycin resistance in Mycobacterium tuberculosis clinical isolates by denaturing high-performance liquid chromatography and DNA sequencing]. (United States)

    Shi, Rui-ru; Zhang, Jian-yuan; Yuan, Xue-qin; Sun, Zhao-gang; Li, Chuan-you


    To determine the rpsL and rrs gene mutation in Mycobacterium tuberculosis (M. tuberculosis) and compare the consistency between the results of denaturing high-performance liquid chromatography (DHPLC) and those of DNA sequencing. The values of streptomycin minimum inhibitory concentration (MIC) against 215 M. tuberculosis clinical isolates, 115 being streptomycin-resistant and 100 being susceptible by a routine proportional method, were tested by DHPLC. DNA sequencing was conducted to detect the rpsL and rrs mutation. 98 of the 115 streptomycin-resistant isolates (85.2%) harbored rpsL and/or rrs mutation, 76.5% of which being rpsL mutation (88/115). There was no significant correlation between the MIC values and mutation types. No mutation was found in all the susceptible isolates. There was a complete consistency between the DHPLC results and those of DNA sequencing. DHPLC can be regarded as a useful and powerful tool to detect the streptomycin resistance detection in M. tuberculosis.

  11. Detection of streptomycin resistance in Mycobacterium tuberculosis clinical isolates from China as determined by denaturing HPLC analysis and DNA sequencing. (United States)

    Shi, Ruiru; Zhang, Jianyuan; Li, Chuanyou; Kazumi, Yuko; Sugawara, Isamu


    China is regarded by the World Health Organization as a major hot-spot region for Mycobacterium tuberculosis infection. Streptomycin has been deployed in China for over 50 years and is still widely used for tuberculosis treatment. We have developed a denaturing HPLC (DHPLC) method for detecting various gene mutations conferring drug resistance in M. tuberculosis. The present study focused on rpsL and rrs mutation analysis. Two hundred and fifteen M. tuberculosis clinical isolates (115 proved to be streptomycin-resistant and 100 susceptible by a routine proportional method) from China were tested to determine the streptomycin minimal inhibitory concentration (MIC), and subjected to DHPLC and concurrent DNA sequencing to determine rpsL and rrs mutations. The results showed that 85.2% (98/115) of streptomycin-resistant isolates harbored rpsL or rrs mutation, while rpsL mutation (76.5%, 88/115) dominated. MIC of 98 mutated isolates revealed no close correlation between mutation types and levels of streptomycin resistance. No mutation was found in any of the susceptible isolates. The DHPLC results were completely consistent with those of sequencing. The DHPLC method devised in this study can be regarded as a useful and powerful tool for detection of streptomycin resistance. This is the first report to describe DHPLC analysis of mutations in the rpsL and rrs genes of M. tuberculosis in a large number of clinical isolates.

  12. Age-related changes in the endocytosis of heat-denatured colloidal albumin by rat Kupffer cells in vitro

    International Nuclear Information System (INIS)

    Brouwer, A.; Barelds, R.J.; Knook, D.L.


    In this study, two major functions of rat liver Kupffer cells, viz., endocytosis and catabolism, were determined in relation to age to investigate the cellular basis of the age-related changes in the functional capacity of the RES. Rat liver Kupffer cells were isolated, purified and placed into maintenance culture for 24 hours. The cells were then incubated with 125 I-labelled heat-denatured colloidal albumin (CA 125 I), a clinically used RES test substance. The kinetics of endocytosis and the catabolism of CA 125 I by Kupffer cells obtained from female BN/BiRij rats of various ages were compared. After incubation of cultured Kupffer cells with various concentrations of CA 125 I, no differences were observed in the uptake of CA 125 I by cells from rats of different ages. The capacities of Kupffer cells from young and old rats to degrade and excrete ingested CA 125 I are compared. Although Kupffer cells from old rats appear to be slightly more effective in the degradation and excretion of CA 125 I during the first half hour of postincubation, no significant differences between the two age groups were observed. (Auth.)

  13. Antiviral Polymer Therapeutics

    DEFF Research Database (Denmark)

    Smith, Anton Allen Abbotsford


    The field of drug delivery is in essence an exercise in engineered pharmacokinetics. Methods of doing so have been developed through the introduction of a vehicle carrying the drug, either by encapsulation or covalent attachment. The emergence of polymer therapeutics in anticancer therapy has...... garnered a great deal of interest due to the substantial room for improvement inherent to conventional chemotherapeutic agents. Chemotherapeutic agents and antiviral agents have a lot of features in common due to both of them typically targeting endogenous targets, unlike antibacterial compounds, though...... the examples of polymer therapeutics being applied as an antiviral treatment are few and far in-between. This work aims to explore antiviral therapeutics, specifically in context of hepatitis virus C (HCV) and HIV. The current treatment of hepatitis C consists of a combination of drugs, of which ribavirin...

  14. Polymer Physics Prize Talk (United States)

    Olvera de La Cruz, Monica

    Polymer electrolytes have been particularly difficult to describe theoretically given the large number of disparate length scales involved in determining their physical properties. The Debye length, the Bjerrum length, the ion size, the chain length, and the distance between the charges along their backbones determine their structure and their response to external fields. We have developed an approach that uses multi-scale calculations with the capability of demonstrating the phase behavior of polymer electrolytes and of providing a conceptual understanding of how charge dictates nano-scale structure formation. Moreover, our molecular dynamics simulations have provided an understanding of the coupling of their conformation to their dynamics, which is crucial to design self-assembling materials, as well as to explore the dynamics of complex electrolytes for energy storage and conversion applications.

  15. Dielectric Actuation of Polymers (United States)

    Niu, Xiaofan

    Dielectric polymers are widely used in a plurality of applications, such as electrical insulation, dielectric capacitors, and electromechanical actuators. Dielectric polymers with large strain deformations under an electric field are named dielectric elastomers (DE), because of their relative low modulus, high elongation at break, and outstanding resilience. Dielectric elastomer actuators (DEA) are superior to traditional transducers as a muscle-like technology: large strains, high energy densities, high coupling efficiency, quiet operation, and light weight. One focus of this dissertation is on the design of DE materials with high performance and easy processing. UV radiation curing of reactive species is studied as a generic synthesis methodology to provide a platform for material scientists to customize their own DE materials. Oligomers/monomers, crosslinkers, and other additives are mixed and cured at appropriate ratios to control the stress-strain response, suppress electromechanical instability of the resulting polymers, and provide stable actuation strains larger than 100% and energy densities higher than 1 J/g. The processing is largely simplified in the new material system by removal of the prestretching step. Multilayer stack actuators with 11% linear strain are demonstrated in a procedure fully compatible with industrial production. A multifunctional DE derivative material, bistable electroactive polymer (BSEP), is invented enabling repeatable rigid-to-rigid deformation without bulky external structures. Bistable actuation allows the polymer actuator to have two distinct states that can support external load without device failure. Plasticizers are used to lower the glass transition temperature to 45 °C. Interpenetrating polymer network structure is established inside the BSEP to suppress electromechanical instability, providing a breakdown field of 194 MV/m and a stable bistable strain as large as 228% with a 97% strain fixity. The application of BSEP

  16. Polymer/Clay Nanocomposites

    Directory of Open Access Journals (Sweden)

    M. Mehrdad shokrieh


    Full Text Available Nanocomposite materials have recently attracted increasing interests in the field of modelling. Finite element modelling can be used for computation of bulk properties of polymer/clay nanocomposites. In this study, by   considering the structure of a nano-composite material, a quasi real model is proposed. The model has been used to predict the elastic constants by selection of suitable elements and boundary conditions. The effects of nano-structural parameters on the mechanical properties of a polymer/clay nano-composite are studied. The geometrical overlap of particles, horizontal distance between particles, length of particles and nano-clay volume fraction are defined as functions of the nano-structural parameters and their effects on mechanical properties of nano-composites are studied by a finite element modelling technique.

  17. Mesoscale Polymer Assemblies (United States)

    Choudhary, Satyan; Pham, Jonathan; Crosby, Alfred


    Materials encompassing structural hierarchy and multi-functionality allow for remarkable physical properties across different length scales. Mesoscale Polymer (MSP) assemblies provide a critical link, from nanometer to centimeter scales, in the definition of such hierarchical structures. Recent focus has been on exploiting these MSP assemblies for optical, electronic, photonics and biological applications. We demonstrate a novel fabrication method for MSP assemblies. Current fabrication methods restrict the length scale and volume of such assemblies. A new method developed uses a simple piezo-actuated motion for de-pinning of a polymer solution trapped by capillary forces between a flexible blade and a rigid substrate. The advantages of new method include ability to make MSP of monodisperse length and to fabricate sufficient volumes of MSP to study their physical properties and functionality in liquid dispersions. We demonstrate the application of MSP as filler for soft materials, providing rheological studies of the MSP with surrounding matrices.

  18. How do polymers degrade? (United States)

    Lyu, Suping


    Materials derived from agricultural products such as cellulose, starch, polylactide, etc. are more sustainable and environmentally benign than those derived from petroleum. However, applications of these polymers are limited by their processing properties, chemical and thermal stabilities. For example, polyethylene terephthalate fabrics last for many years under normal use conditions, but polylactide fabrics cannot due to chemical degradation. There are two primary mechanisms through which these polymers degrade: via hydrolysis and via oxidation. Both of these two mechanisms are related to combined factors such as monomer chemistry, chain configuration, chain mobility, crystallinity, and permeation to water and oxygen, and product geometry. In this talk, we will discuss how these materials degrade and how the degradation depends on these factors under application conditions. Both experimental studies and mathematical modeling will be presented.

  19. Conjugated polymer nanoparticles, methods of using, and methods of making

    KAUST Repository

    Habuchi, Satoshi


    Embodiments of the present disclosure provide for conjugated polymer nanoparticle, method of making conjugated polymer nanoparticles, method of using conjugated polymer nanoparticle, polymers, and the like.

  20. Knots in polymers

    Indian Academy of Sciences (India)

    Ey; 05.40.Fb; 02.10.Kn; 82.35.Rs. 1. Introduction. Knots and links naturally appear in long polymers [1] and play an important role in biological processes [2]. The simplest statistical–mechanical model of a ..... [6] A D Bates and A Maxwell, DNA Topology (IRL Press, Oxford, 1993). [7] P Pieranski, S Przyby l and A Stasiak, ...

  1. Electrochemical polymer electrolyte membranes

    CERN Document Server

    Fang, Jianhua; Wilkinson, David P


    Electrochemical Polymer Electrolyte Membranes covers PEMs from fundamentals to applications, describing their structure, properties, characterization, synthesis, and use in electrochemical energy storage and solar energy conversion technologies. Featuring chapters authored by leading experts from academia and industry, this authoritative text: Discusses cutting-edge methodologies in PEM material selection and fabricationPoints out important challenges in developing PEMs and recommends mitigation strategies to improve PEM performanceAnalyzes the cur

  2. Solid polymer electrolytes (United States)

    Abraham, Kuzhikalail M.; Alamgir, Mohamed; Choe, Hyoun S.


    This invention relates to Li ion (Li.sup.+) conductive solid polymer electrolytes composed of poly(vinyl sulfone) and lithium salts, and their use in all-solid-state rechargeable lithium ion batteries. The lithium salts comprise low lattice energy lithium salts such as LiN(CF.sub.3 SO.sub.2).sub.2, LiAsF.sub.6, and LiClO.sub.4.

  3. Dynamics of polymers

    Energy Technology Data Exchange (ETDEWEB)

    Buchenau, U. [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Energieverfahrenstechnik


    Neutron scattering from amorphous polymers allows to switch from incoherent to coherent scattering in the same substance. The power of the tool for the study of the picosecond dynamics of disordered matter is illustrated for polybutadiene, polycarbonate and polystyrene. The results suggest a mixture of sound waves and localized modes, strongly interacting with each other, in the picosecond range. (author) 8 figs., tabs., 39 refs.

  4. High Mobility Conjugated Polymers (United States)


    blends with poly(3- hexylthiophene) (PHT) could be readily fabricated as uniform nanofibers by co- electrospinning their solutions with another solution...We have demonstrated that nanofibers of conjugated 10 - polymers and their blends could be conveniently fabricated by electrospinning . Furthermore, we...luminance o - - characteristics of an ITO/ PEDOT /TAPC k D r a Vol gt, V, (V) /BPQ-PPO/LiF/A! device are shown in Fig. 30. (A) Current density-voltage

  5. Dynamics of polymers

    International Nuclear Information System (INIS)

    Buchenau, U.


    Neutron scattering from amorphous polymers allows to switch from incoherent to coherent scattering in the same substance. The power of the tool for the study of the picosecond dynamics of disordered matter is illustrated for polybutadiene, polycarbonate and polystyrene. The results suggest a mixture of sound waves and localized modes, strongly interacting with each other, in the picosecond range. (author) 8 figs., tabs., 39 refs


    Directory of Open Access Journals (Sweden)

    I. I. Karpunin


    Full Text Available The executed investigations have made it possible to ascertain that a morphological structure of starch granules mainly determine technological peculiarities of starch isolation from raw material, its modification and its later use. Morphological structure of starch granules primarily depends on type of plant starch-containing raw material which has been used for its isolation. Class of raw material exerts a strong impact on the shape and size of the granules. Linear “light” amylose chains and “heavy” amylopectin branch chains form a starch granule ultrastructure. X-ray research has proved that starch granules are characterized by presence of interlacing amorphous and crystalline regions. In this case polymer orientation using stretching of the obtained end product influences on its physical and mechanical  indices which are increasing due to polymer orientation. For the purpose of packaging orientation of polymer films can solve such important problems as significant improvement of operational properties, creation of  thermosetting film materials, improvement of qualitative indices of the recycled film.Results of the conducted research have proved the fact that it is necessary to make changes in technology in order to increase biological degradability of the recycled packaging made from polymers and improve physical and mechanical indices. In this regard film production technology presupposes usage of such substances as stark and others which are characterized by rather large presence of branch chains of molecules and interlacing amorphous and crystalline regions. Such approach makes it possible to obtain after-use package which is strong and quickly degradable by micro-organisms.

  7. Polymer engineering (I)

    International Nuclear Information System (INIS)

    Kim, Seong Cheol; Kim, Do Hyeon; Lee, Gi Yun


    This book deals with polymer engineering, which gives descriptions of addition polymerization, condensation polymerization, special polymerization, copolymerization, reaction of a high molecule, polymerization process, structure of a high molecule chain, molecular weight, crystal structure of a high molecule, melting and glass transition, viscoelasticity of a high molecule, rubber elasticity, transform and destroy of a high molecule, property of another matter, melting rheology of a high molecule, flowing in the tube and channel, pressing, injection molding, calendaring and spinning process.

  8. Absorbable and biodegradable polymers

    CERN Document Server

    Shalaby, Shalaby W


    INTRODUCTION NOTES: Absorbable/Biodegradable Polymers: Technology Evolution. DEVELOPMENT AND APPLICATIONOF NEW SYSTEMS: Segmented Copolyesters with Prolonged Strength Retention Profiles. Polyaxial Crystalline Fiber-Forming Copolyester. Polyethylene Glycol-Based Copolyesters. Cyanoacrylate-Based Systems as Tissue Adhesives. Chitosan-Based Systems. Hyaluronic Acid-Based Systems. DEVELOPMENTS IN PREPARATIVE, PROCESSING, AND EVALUATION METHODS: New Approaches to the Synthesis of Crystalline. Fiber-Forming Aliphatic Copolyesters. Advances in Morphological Development to Tailor the Performance of Me

  9. Conductive Polymer Composites


    Pierini, Filippo


    In recent years, nanotechnologies have led to the production of materials with new and sometimes unexpected qualities through the manipulation of nanoscale components. This research aimed primarily to the study of the correlation between hierarchical structures of hybrid organic-inorganic materials such as conductive polymer composites (CPCs). Using a bottom-up methodology, we could synthesize a wide range of inorganic nanometric materials with a high degree of homogeneity and purity, ...

  10. Enhancement of Polymer Cytocompatibility by Nanostructuring of Polymer Surface

    Directory of Open Access Journals (Sweden)

    Petr Slepička


    Full Text Available Polymers with their advantageous physical, chemical, mechanical, and electrical properties and easy manufacturing are widely used in biology, tissue engineering, and medicine, for example, as prosthetic materials. In some cases the polymer usage may be impeded by low biocompatibility of common synthetic polymers. The biocompatibility can be improved by modification of polymer surface, for example, by plasma discharge, irradiation with ionizing radiation, and sometime subsequent grafting with suitable organic (e.g., amino-acids or inorganic (e.g., gold nanoparticles agents. In this way new chemically active structures are created on the polymer surface, and in some cases new surface relief is created. Recent advances in nanotechnology and in characterization of nanostructured objects open the way to development of new polymer-based materials with better bio-properties and higher application potential in biomedicine. Some of recent results obtained in the field are summarized and discussed in this paper.

  11. All-Polymer Lasers (United States)

    Wu, Yeheng; Lott, Joseph; Kazmierczak, Tomasz; Song, Hyunmin; Baer, Eric; Singer, Kenneth; Weder, Christoph


    We have fabricated all-polymer lasers both as distributed feedback lasers (DFB) and distributed Bragg reflector (DBR) lasers. For the DBR lasers, a layer of polymer doped with the laser dye is laminated between two multilayer polymer mirrors. The mirrors were made using the co-extrusion process combining PMMA alternated with polystyrene with 128 layers for each mirror. Two dyes were employed, Rhodamine 6G (R6G), and 1,4-bis-(α-cyano-4-methoxystyryl)-2,5-dimethoxybenzene (C1RG). They were pumped with a nanosecond laser and emitted at about 570 and 510 nm respectively. For DFB lasers, the low refractive index layers were doped with C1RG or R6G. PMMA and PMMA-PVDF were the hosts for the C1RG and R6G respectively. A total of eight co-extruded 32-layer films were stacked together to make a DFB laser. For the DBR lasers, we were able to observe thresholds as low as 100nJ. The highest conversion efficiency obtained about 14% in the forward direction. We also observed trends of lasing threshold, even spaced lasing modes and penetration of the film. Matrix method simulations taking into account layer thickness variations were consistent with experimental results. For the DFB lasers, the lowest lasing threshold observed was 52 μW.

  12. Simulated Associating Polymer Networks (United States)

    Billen, Joris

    Telechelic associating polymer networks consist of polymer chains terminated by endgroups that have a different chemical composition than the polymer backbone. When dissolved in a solution, the endgroups cluster together to form aggregates. At low temperature, a strongly connected reversible network is formed and the system behaves like a gel. Telechelic networks are of interest since they are representative for biopolymer networks (e.g. F-actin) and are widely used in medical applications (e.g. hydrogels for tissue engineering, wound dressings) and consumer products (e.g. contact lenses, paint thickeners). In this thesis such systems are studied by means of a molecular dynamics/Monte Carlo simulation. At first, the system in rest is studied by means of graph theory. The changes in network topology upon cooling to the gel state, are characterized. Hereto an extensive study of the eigenvalue spectrum of the gel network is performed. As a result, an in-depth investigation of the eigenvalue spectra for spatial ER, scale-free, and small-world networks is carried out. Next, the gel under the application of a constant shear is studied, with a focus on shear banding and the changes in topology under shear. Finally, the relation between the gel transition and percolation is discussed.

  13. BioArtificial polymers (United States)

    Szałata, Kamila; Gumi, Tania


    Nowadays, the polymer science has impact in practically all life areas. Countless benefits coming from the usage of materials with high mechanical and chemical resistance, variety of functionalities and potentiality of modification drive to the development of new application fields. Novel approaches of combining these synthetic substances with biomolecules lead to obtain multifunctional hybrid conjugates which merge the bioactivity of natural component with outstanding properties of artificial polymer. Over the decades, an immense progress in bioartificial composites domain allowed to reach a high level of knowledge in terms of natural-like systems engineering, leading to diverse strategies of biomolecule immobilization. Together with different available options, including covalent and noncovalent attachment, come various challenges, related mainly with maintaining the biological activity of fixed molecules. Even though the amount of applications that achieve commercial status is still not substantial, and is expanding continuously in the disciplines like "smart materials," biosensors, delivery systems, nanoreactors and many others. A huge number of remarkable developments reported in the literature present a potential of bioartificial conjugates as a fabrics with highly controllable structure and multiple functionalities, serving as a powerful nanotechnological tool. This novel approach brings closer biologists, chemists and engineers, who sharing their effort and complementing the knowledge can revolutionize the field of bioartificial polymer science.

  14. Polymer structure database and protein-polymer interactions

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich; Labský, Jiří; Skálová, Tereza; Kolenko, Petr; Dohnálek, Jan; Dušková, Jarmila; Štěpánková, Andrea; Koval, T.

    -, č. 1 (2011), s. 475-480 ISSN 1869-1315. [European Powder Diffraction Conference EPDIC 12 /12./. Darmstadt, 27.08.2010-30.08.2010] R&D Projects: GA ČR GA305/07/1073; GA AV ČR IAA500500701 Institutional research plan: CEZ:AV0Z40500505 Keywords : hydrophilic polymers * crystalline polymers * adhesion of polymers Subject RIV: CD - Macromolecular Chemistry

  15. Thermodynamic characterization of cytochrome c at low pH. Observation of the molten globule state and of the cold denaturation process. (United States)

    Kuroda, Y; Kidokoro, S; Wada, A


    Several reports have pointed out the existence of intermediate states (both kinetic and equilibrium intermediate) between the native and the denatured states. The molten globule state, a compact intermediate state in which the secondary structure is formed but the tertiary structure fluctuates considerably, is currently being studied intensively because of its possible implication in the folding process of several proteins. We have examined the thermal stability of horse cytochrome c at low pH between 2.0 and 3.2 and different potassium chloride concentrations by absorbance of the Soret band, far and near-ultraviolet circular dichroism (u.v. c.d.) and tryptophan fluorescence using a multidimensional spectrophotometer. The concentration of potassium chloride ranged from 0 M to 0.5 M. The experimental thermal denaturation curves show that: (1) the helical content of cytochrome c remains stable at higher temperature when the concentration of salt is increased; whereas (2) the extent of ordering of the tertiary structure is weakly dependent on salt concentration; and (3) for cytochrome c, the stabilization of the molten globule state is induced by the binding of anions. Other salts such as NaCl, LiCl, potassium ferricyanide (K3Fe(CN)6) and Na2SO4 may also be used to stabilize the molten globule state. The thermodynamic analysis of the denaturation curves of c.d. at 222 nm and c.d. at 282 nm shows that, whereas a two-state (native and denatured) transition is observed at low-salt concentration, the far and near-u.v. c.d. melting curves of cytochrome c do not coincide with each other at high-salt concentration, and a minimum of three different thermodynamic states (IIb, intermediate or IIc, and denatured) is necessary to achieve a sufficient analysis. The intermediate state (called IIc) is attributed to the molten globule state because of its high secondary structure content and the absence of tertiary structure. Therefore, at low pH, cytochrome c is present in at least

  16. Fabrication and characterization of polymer blends and composites derived from biopolymers (United States)

    Sharma, Suraj

    This research focuses on fabricating blends and composites from natural polymers especially from proteins and natural epoxy, and describing the properties of plastics made from them. Specifically, plastic samples from partially denatured feathermeal and bloodmeal proteins, derived from the animal co-products (rendering) industry, were successfully produced through a compression molding process. The modulus (stiffness) of the material obtained was found to be comparable with that of commercial synthetic materials, such as polystyrene, but was found to have lower toughness characteristics, which is a common phenomenon among plastics produced from animal and plant proteins. Therefore, this study explored blending methods for improving the toughness. Plastic forming conditions for undenatured animal proteins such as chicken egg whites albumin and whey, used as a model, were established to prepare plastics from their blends with animal co-product proteins. The resultant plastic samples from these biomacromolecular blends demonstrated improved mechanical properties that were also compared with the established theoretical models known for polymer blends and composites. Moreover, plastics from albumin of chicken egg whites and human serum have demonstrated their potential in medical applications that require antibacterial properties. Another natural polymer vegetable oil-based epoxy, especially epoxidized linseed oil, showed significant potential to replace petroleum-derived resins for use as a matrix for composites in structural applications. Moreover, the research showed the benefits of ultrasonic curing, which can help in preparing the out-of-autoclave composites.

  17. Writing on polymer chains. (United States)

    Lutz, Jean-François


    Synthetic polymer materials are currently limited by their inability to store information in their chains, unlike some well-characterized biopolymers. Nucleic acids store and transmit genetic information, and amino acids encode the complex tridimensional structures and functions within proteins. To confer similar properties on synthetic materials, researchers must develop"writing" mechanisms, facile chemical pathways that allow control over the primary structure of synthetic polymer chains. The most obvious way to control the primary structure is to connect monomer units one-by-one in a given order using iterative chemistry. Although such synthesis strategies are commonly used to produce peptides and nucleic acids, they produce limited yields and are much slower than natural polymerization mechanisms. An alternative strategy would be to use multiblock copolymers with blocks that have specified sequences. In this case, however, the basic storage element is not a single molecular unit, but a longer block composed of several repeating units. However, the synthesis of multiblock copolymers is long and tedious. Therefore, researchers will need to develop other strategies for writing information onto polymer chains. In this Account, I describe our recent progress in the development of sequence controlled polymerization methods. Although our research focuses on different strategies, we have emphasized sequence-regulation in chain-growth polymerization processes. Chain-growth polymerizations, particularly radical polymerization, are very convenient methods for synthesizing polymers. However, in most cases, such approaches do not lead to controlled monomer sequences. During the last five years, we have shown that controlled/living chain-growth polymerization mechanisms offer interesting advantages for sequence regulation. In such mechanisms, the chains form gradually over time, and therefore the primary structure can be tuned by using time-controlled monomer additions. For

  18. Synthetic approaches to uniform polymers. (United States)

    Ali, Monzur; Brocchini, Steve


    Uniform polymers are characterised by a narrow molecular weight distribution (MWD). Uniformity is also defined by chemical structure in respect of (1) monomer orientation, sequence and stereo-regularity, (2) polymer shape and morphology and (3) chemical functionality. The function of natural polymers such as polypeptides and polynucleotides is related to their conformational structure (e.g. folded tertiary structure). This is only possible because of their high degree of uniformity. While completely uniform synthetic polymers are rare, polymers with broad structure and MWD are widely used in medicine and the biomedical sciences. They are integral components in final dosage forms, drug delivery systems (DDS) and in implantable devices. Increasingly uniform polymers are being used to develop more complex medicines (e.g. delivery of biopharmaceuticals, enhanced formulations or DDS's for existing actives). In addition to the function imparted by any new polymer it will be required to meet stringent specifications in terms of cost containment, scalability, biocompatibility and performance. Synthetic polymers with therapeutic activity are also being developed to exploit their polyvalent properties, which is not possible with low molecular weight molecules. There is need to utilise uniform polymers for applications where the polymer may interact with the systemic circulation, tissues or cellular environment. There are also potential applications (e.g. stimuli responsive coatings) where uniform polymers may be used for their more defined property profile. While it is not yet practical to prepare synthetic polymers to the same high degree of uniformity as proteins, nature also effectively utilises many polymers with lower degrees of uniformity (e.g. polysaccharides, poly(amino acids), polyhydroxyalkanoates). In recent years it has become possible to prepare with practical experimental protocols sufficient quantities of polymers that display many aspects of uniformity. This

  19. Purification of correctly oxidized MHC class I heavy-chain molecules under denaturing conditions: A novel strategy exploiting disulfide assisted protein folding

    DEFF Research Database (Denmark)

    Ferré, Henrik; Ruffet, E.; Blicher, T.


    The aim of this study has been to develop a strategy for purifying correctly oxidized denatured major histocompability complex class I (MHC-I) heavy-chain molecules, which on dilution, fold efficiently and become functional. Expression of heavy-chain molecules in bacteria results in the formation......)-microglobulin and a specific peptide. Under conditions optimized for peptide binding, refolding and simultaneous peptide binding of the correctly oxidized heavy chain was much more efficient than that of the fully reduced molecule....

  20. Purification of correctly oxidized MHC class I heavy-chain molecules under denaturing conditions: a novel strategy exploiting disulfide assisted protein folding

    DEFF Research Database (Denmark)

    Ferré, Henrik; Ruffet, Emmanuel; Blicher, Thomas


    The aim of this study has been to develop a strategy for purifying correctly oxidized denatured major histocompability complex class I (MHC-I) heavy-chain molecules, which on dilution, fold efficiently and become functional. Expression of heavy-chain molecules in bacteria results in the formation......(2)-microglobulin and a specific peptide. Under conditions optimized for peptide binding, refolding and simultaneous peptide binding of the correctly oxidized heavy chain was much more efficient than that of the fully reduced molecule....